getwd()
[1] "/Users/baharsevgin/Desktop/Omics Data Analysis/RNAseq(DE) practical"
knitr::opts_chunk$set(echo = TRUE)
Error in loadNamespace(x) : there is no package called ‘knitr’
 if (!requireNamespace("BiocManager", quietly = TRUE))
     install.packages("BiocManager")
Warning in install.packages :
  lzma decoder corrupt data

  There is a binary version available but the source version is later:
installing the source package ‘BiocManager’

trying URL 'https://cran.rstudio.com/src/contrib/BiocManager_1.30.26.tar.gz'
Content type 'application/x-gzip' length 594489 bytes (580 KB)
==================================================
downloaded 580 KB

* installing *source* package ‘BiocManager’ ...
** package ‘BiocManager’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BiocManager)

The downloaded source packages are in
    ‘/private/var/folders/db/_9mqvxh50pb53z2xy8z_xhjr0000gn/T/RtmpXjWyRf/downloaded_packages’
BiocManager::install("DESeq2", version = "3.14")
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cran.rstudio.com/
Bioconductor version 3.14 (BiocManager 1.30.26), R 4.1.3 (2022-03-10)
Installing package(s) 'BiocVersion', 'DESeq2'
also installing the dependencies ‘fastmap’, ‘sys’, ‘bit’, ‘cachem’, ‘crayon’, ‘askpass’, ‘bitops’, ‘formatR’, ‘bit64’, ‘blob’, ‘memoise’, ‘plogr’, ‘cpp11’, ‘png’, ‘Biostrings’, ‘curl’, ‘jsonlite’, ‘mime’, ‘openssl’, ‘utf8’, ‘RCurl’, ‘GenomeInfoDbData’, ‘zlibbioc’, ‘matrixStats’, ‘lambda.r’, ‘futile.options’, ‘DBI’, ‘RSQLite’, ‘KEGGREST’, ‘XML’, ‘xtable’, ‘httr’, ‘farver’, ‘labeling’, ‘R6’, ‘viridisLite’, ‘magrittr’, ‘pillar’, ‘pkgconfig’, ‘GenomeInfoDb’, ‘XVector’, ‘MatrixGenerics’, ‘DelayedArray’, ‘futile.logger’, ‘snow’, ‘BH’, ‘AnnotationDbi’, ‘annotate’, ‘RColorBrewer’, ‘cli’, ‘glue’, ‘gtable’, ‘isoband’, ‘lifecycle’, ‘rlang’, ‘scales’, ‘tibble’, ‘vctrs’, ‘withr’, ‘S4Vectors’, ‘IRanges’, ‘GenomicRanges’, ‘SummarizedExperiment’, ‘BiocGenerics’, ‘Biobase’, ‘BiocParallel’, ‘genefilter’, ‘locfit’, ‘geneplotter’, ‘ggplot2’, ‘Rcpp’, ‘RcppArmadillo’

Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/data/annotation/bin/macosx/contrib/4.1/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/data/annotation/bin/macosx/contrib/4.1/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/data/experiment/bin/macosx/contrib/4.1/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/data/experiment/bin/macosx/contrib/4.1/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/workflows/bin/macosx/contrib/4.1/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/workflows/bin/macosx/contrib/4.1/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 11573Warning: cannot open URL 'https://bioconductor.org/packages/3.14/books/bin/macosx/contrib/4.1/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 11573Warning: cannot open URL 'https://bioconductor.org/packages/3.14/books/bin/macosx/contrib/4.1/PACKAGES.gz': HTTP status was '404 Not Found'

  There are binary versions available but the source versions are later:
no
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/fastmap_1.1.1.tgz'
Content type 'application/x-gzip' length 201256 bytes (196 KB)
==================================================
downloaded 196 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/sys_3.4.1.tgz'
Content type 'application/x-gzip' length 47312 bytes (46 KB)
==================================================
downloaded 46 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/bit_4.0.5.tgz'
Content type 'application/x-gzip' length 1243615 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/cachem_1.0.8.tgz'
Content type 'application/x-gzip' length 67489 bytes (65 KB)
==================================================
downloaded 65 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/askpass_1.1.tgz'
Content type 'application/x-gzip' length 21566 bytes (21 KB)
==================================================
downloaded 21 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/bitops_1.0-7.tgz'
Content type 'application/x-gzip' length 29174 bytes (28 KB)
==================================================
downloaded 28 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/formatR_1.14.tgz'
Content type 'application/x-gzip' length 149645 bytes (146 KB)
==================================================
downloaded 146 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/bit64_4.0.5.tgz'
Content type 'application/x-gzip' length 576409 bytes (562 KB)
==================================================
downloaded 562 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/blob_1.2.4.tgz'
Content type 'application/x-gzip' length 46270 bytes (45 KB)
==================================================
downloaded 45 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/memoise_2.0.1.tgz'
Content type 'application/x-gzip' length 48111 bytes (46 KB)
==================================================
downloaded 46 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/plogr_0.2.0.tgz'
Content type 'application/x-gzip' length 12964 bytes (12 KB)
==================================================
downloaded 12 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/png_0.1-8.tgz'
Content type 'application/x-gzip' length 369995 bytes (361 KB)
==================================================
downloaded 361 KB

trying URL 'https://bioconductor.org/packages/3.14/bioc/bin/macosx/contrib/4.1/Biostrings_2.62.0.tgz'
Content type 'application/octet-stream' length 14241415 bytes (13.6 MB)
==================================================
downloaded 13.6 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/curl_5.0.0.tgz'
Content type 'application/x-gzip' length 759005 bytes (741 KB)
==================================================
downloaded 741 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/jsonlite_1.8.4.tgz'
Content type 'application/x-gzip' length 1113981 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/mime_0.12.tgz'
Content type 'application/x-gzip' length 34812 bytes (33 KB)
==================================================
downloaded 33 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/openssl_2.0.6.tgz'
Content type 'application/x-gzip' length 2886168 bytes (2.8 MB)
==================================================
downloaded 2.8 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/utf8_1.2.3.tgz'
Content type 'application/x-gzip' length 196912 bytes (192 KB)
==================================================
downloaded 192 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/RCurl_1.98-1.12.tgz'
Content type 'application/x-gzip' length 1089009 bytes (1.0 MB)
==================================================
downloaded 1.0 MB

trying URL 'https://bioconductor.org/packages/3.14/bioc/bin/macosx/contrib/4.1/zlibbioc_1.40.0.tgz'
Content type 'application/octet-stream' length 125768 bytes (122 KB)
==================================================
downloaded 122 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/matrixStats_0.63.0.tgz'
Content type 'application/x-gzip' length 592172 bytes (578 KB)
==================================================
downloaded 578 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/lambda.r_1.2.4.tgz'
Content type 'application/x-gzip' length 109754 bytes (107 KB)
==================================================
downloaded 107 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/futile.options_1.0.1.tgz'
Content type 'application/x-gzip' length 18137 bytes (17 KB)
==================================================
downloaded 17 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/RSQLite_2.3.1.tgz'
Content type 'application/x-gzip' length 4340278 bytes (4.1 MB)
==================================================
downloaded 4.1 MB

trying URL 'https://bioconductor.org/packages/3.14/bioc/bin/macosx/contrib/4.1/KEGGREST_1.34.0.tgz'
Content type 'application/octet-stream' length 184843 bytes (180 KB)
==================================================
downloaded 180 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/XML_3.99-0.14.tgz'
Content type 'application/x-gzip' length 1873852 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/xtable_1.8-4.tgz'
Content type 'application/x-gzip' length 701448 bytes (685 KB)
==================================================
downloaded 685 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/farver_2.1.1.tgz'
Content type 'application/x-gzip' length 1943005 bytes (1.9 MB)
==================================================
downloaded 1.9 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/viridisLite_0.4.2.tgz'
Content type 'application/x-gzip' length 1297080 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/magrittr_2.0.3.tgz'
Content type 'application/x-gzip' length 227497 bytes (222 KB)
==================================================
downloaded 222 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/pkgconfig_2.0.3.tgz'
Content type 'application/x-gzip' length 17777 bytes (17 KB)
==================================================
downloaded 17 KB

trying URL 'https://bioconductor.org/packages/3.14/bioc/bin/macosx/contrib/4.1/GenomeInfoDb_1.30.1.tgz'
Content type 'application/octet-stream' length 4033747 bytes (3.8 MB)
==================================================
downloaded 3.8 MB

trying URL 'https://bioconductor.org/packages/3.14/bioc/bin/macosx/contrib/4.1/XVector_0.34.0.tgz'
Content type 'application/octet-stream' length 625655 bytes (610 KB)
==================================================
downloaded 610 KB

trying URL 'https://bioconductor.org/packages/3.14/bioc/bin/macosx/contrib/4.1/MatrixGenerics_1.6.0.tgz'
Content type 'application/octet-stream' length 310558 bytes (303 KB)
==================================================
downloaded 303 KB

trying URL 'https://bioconductor.org/packages/3.14/bioc/bin/macosx/contrib/4.1/DelayedArray_0.20.0.tgz'
Content type 'application/octet-stream' length 2486317 bytes (2.4 MB)
==================================================
downloaded 2.4 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/futile.logger_1.4.3.tgz'
Content type 'application/x-gzip' length 95382 bytes (93 KB)
==================================================
downloaded 93 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/snow_0.4-4.tgz'
Content type 'application/x-gzip' length 95840 bytes (93 KB)
==================================================
downloaded 93 KB

trying URL 'https://bioconductor.org/packages/3.14/bioc/bin/macosx/contrib/4.1/AnnotationDbi_1.56.2.tgz'
Content type 'application/octet-stream' length 5170378 bytes (4.9 MB)
==================================================
downloaded 4.9 MB

trying URL 'https://bioconductor.org/packages/3.14/bioc/bin/macosx/contrib/4.1/annotate_1.72.0.tgz'
Content type 'application/octet-stream' length 2081366 bytes (2.0 MB)
==================================================
downloaded 2.0 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/RColorBrewer_1.1-3.tgz'
Content type 'application/x-gzip' length 53237 bytes (51 KB)
==================================================
downloaded 51 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/cli_3.6.1.tgz'
Content type 'application/x-gzip' length 1365687 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/glue_1.6.2.tgz'
Content type 'application/x-gzip' length 151977 bytes (148 KB)
==================================================
downloaded 148 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/isoband_0.2.7.tgz'
Content type 'application/x-gzip' length 1869529 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/rlang_1.1.1.tgz'
Content type 'application/x-gzip' length 1852475 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/tibble_3.2.1.tgz'
Content type 'application/x-gzip' length 676416 bytes (660 KB)
==================================================
downloaded 660 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/vctrs_0.6.2.tgz'
Content type 'application/x-gzip' length 1850681 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

trying URL 'https://bioconductor.org/packages/3.14/bioc/bin/macosx/contrib/4.1/S4Vectors_0.32.4.tgz'
Content type 'application/octet-stream' length 2102831 bytes (2.0 MB)
==================================================
downloaded 2.0 MB

trying URL 'https://bioconductor.org/packages/3.14/bioc/bin/macosx/contrib/4.1/IRanges_2.28.0.tgz'
Content type 'application/octet-stream' length 2254035 bytes (2.1 MB)
==================================================
downloaded 2.1 MB

trying URL 'https://bioconductor.org/packages/3.14/bioc/bin/macosx/contrib/4.1/GenomicRanges_1.46.1.tgz'
Content type 'application/octet-stream' length 2159608 bytes (2.1 MB)
==================================================
downloaded 2.1 MB

trying URL 'https://bioconductor.org/packages/3.14/bioc/bin/macosx/contrib/4.1/SummarizedExperiment_1.24.0.tgz'
Content type 'application/octet-stream' length 2826362 bytes (2.7 MB)
==================================================
downloaded 2.7 MB

trying URL 'https://bioconductor.org/packages/3.14/bioc/bin/macosx/contrib/4.1/BiocGenerics_0.40.0.tgz'
Content type 'application/octet-stream' length 589888 bytes (576 KB)
==================================================
downloaded 576 KB

trying URL 'https://bioconductor.org/packages/3.14/bioc/bin/macosx/contrib/4.1/Biobase_2.54.0.tgz'
Content type 'application/octet-stream' length 2342979 bytes (2.2 MB)
==================================================
downloaded 2.2 MB

trying URL 'https://bioconductor.org/packages/3.14/bioc/bin/macosx/contrib/4.1/BiocParallel_1.28.3.tgz'
Content type 'application/octet-stream' length 1375804 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

trying URL 'https://bioconductor.org/packages/3.14/bioc/bin/macosx/contrib/4.1/genefilter_1.76.0.tgz'
Content type 'application/octet-stream' length 1227189 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/locfit_1.5-9.7.tgz'
Content type 'application/x-gzip' length 772384 bytes (754 KB)
==================================================
downloaded 754 KB

trying URL 'https://bioconductor.org/packages/3.14/bioc/bin/macosx/contrib/4.1/geneplotter_1.72.0.tgz'
Content type 'application/octet-stream' length 1557999 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/Rcpp_1.0.10.tgz'
Content type 'application/x-gzip' length 3242867 bytes (3.1 MB)
==================================================
downloaded 3.1 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/RcppArmadillo_0.12.2.0.0.tgz'
Content type 'application/x-gzip' length 1570686 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

trying URL 'https://bioconductor.org/packages/3.14/bioc/bin/macosx/contrib/4.1/BiocVersion_3.14.0.tgz'
Content type 'application/octet-stream' length 5532 bytes
==================================================
downloaded 5532 bytes

trying URL 'https://bioconductor.org/packages/3.14/bioc/bin/macosx/contrib/4.1/DESeq2_1.34.0.tgz'
Content type 'application/octet-stream' length 2781761 bytes (2.7 MB)
==================================================
downloaded 2.7 MB

The downloaded binary packages are in
    /var/folders/db/_9mqvxh50pb53z2xy8z_xhjr0000gn/T//RtmpXjWyRf/downloaded_packages
installing the source packages ‘crayon’, ‘cpp11’, ‘GenomeInfoDbData’, ‘DBI’, ‘httr’, ‘labeling’, ‘R6’, ‘pillar’, ‘BH’, ‘gtable’, ‘lifecycle’, ‘scales’, ‘withr’, ‘ggplot2’

trying URL 'https://cran.rstudio.com/src/contrib/crayon_1.5.3.tar.gz'
Content type 'application/x-gzip' length 40396 bytes (39 KB)
==================================================
downloaded 39 KB

trying URL 'https://cran.rstudio.com/src/contrib/cpp11_0.5.2.tar.gz'
Content type 'application/x-gzip' length 291993 bytes (285 KB)
==================================================
downloaded 285 KB

trying URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/GenomeInfoDbData_1.2.7.tar.gz'
Content type 'application/octet-stream' length 11193674 bytes (10.7 MB)
==================================================
downloaded 10.7 MB

trying URL 'https://cran.rstudio.com/src/contrib/DBI_1.2.3.tar.gz'
Content type 'application/x-gzip' length 1137307 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

trying URL 'https://cran.rstudio.com/src/contrib/httr_1.4.7.tar.gz'
Content type 'application/x-gzip' length 118500 bytes (115 KB)
==================================================
downloaded 115 KB

trying URL 'https://cran.rstudio.com/src/contrib/labeling_0.4.3.tar.gz'
Content type 'application/x-gzip' length 10167 bytes
==================================================
downloaded 10167 bytes

trying URL 'https://cran.rstudio.com/src/contrib/R6_2.6.1.tar.gz'
Content type 'application/x-gzip' length 64507 bytes (62 KB)
==================================================
downloaded 62 KB

trying URL 'https://cran.rstudio.com/src/contrib/pillar_1.11.0.tar.gz'
Content type 'application/x-gzip' length 409321 bytes (399 KB)
==================================================
downloaded 399 KB

trying URL 'https://cran.rstudio.com/src/contrib/BH_1.87.0-1.tar.gz'
Content type 'application/x-gzip' length 14335542 bytes (13.7 MB)
==================================================
downloaded 13.7 MB

trying URL 'https://cran.rstudio.com/src/contrib/gtable_0.3.6.tar.gz'
Content type 'application/x-gzip' length 148148 bytes (144 KB)
==================================================
downloaded 144 KB

trying URL 'https://cran.rstudio.com/src/contrib/lifecycle_1.0.4.tar.gz'
Content type 'application/x-gzip' length 107656 bytes (105 KB)
==================================================
downloaded 105 KB

trying URL 'https://cran.rstudio.com/src/contrib/scales_1.4.0.tar.gz'
Content type 'application/x-gzip' length 328671 bytes (320 KB)
==================================================
downloaded 320 KB

trying URL 'https://cran.rstudio.com/src/contrib/withr_3.0.2.tar.gz'
Content type 'application/x-gzip' length 103240 bytes (100 KB)
==================================================
downloaded 100 KB

trying URL 'https://cran.rstudio.com/src/contrib/ggplot2_3.5.2.tar.gz'
Content type 'application/x-gzip' length 3580451 bytes (3.4 MB)
==================================================
downloaded 3.4 MB

* installing *source* package ‘crayon’ ...
** package ‘crayon’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (crayon)
* installing *source* package ‘cpp11’ ...
** package ‘cpp11’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (cpp11)
* installing *source* package ‘GenomeInfoDbData’ ...
** using staged installation
** data
** inst
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GenomeInfoDbData)
* installing *source* package ‘DBI’ ...
** package ‘DBI’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DBI)
* installing *source* package ‘labeling’ ...
** package ‘labeling’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (labeling)
* installing *source* package ‘R6’ ...
** package ‘R6’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (R6)
* installing *source* package ‘BH’ ...
** package ‘BH’ successfully unpacked and MD5 sums checked
** using staged installation
** inst
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BH)
* installing *source* package ‘lifecycle’ ...
** package ‘lifecycle’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (lifecycle)
* installing *source* package ‘withr’ ...
** package ‘withr’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (withr)
* installing *source* package ‘httr’ ...
** package ‘httr’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (httr)
* installing *source* package ‘pillar’ ...
** package ‘pillar’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (pillar)
* installing *source* package ‘gtable’ ...
** package ‘gtable’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (gtable)
* installing *source* package ‘scales’ ...
** package ‘scales’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (scales)
* installing *source* package ‘ggplot2’ ...
** package ‘ggplot2’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ggplot2)

The downloaded source packages are in
    ‘/private/var/folders/db/_9mqvxh50pb53z2xy8z_xhjr0000gn/T/RtmpXjWyRf/downloaded_packages’
Old packages: 'askpass', 'bit', 'bit64', 'bitops', 'boot', 'cachem', 'class', 'cli', 'cluster', 'codetools', 'curl', 'farver',
  'fastmap', 'foreign', 'glue', 'jsonlite', 'KernSmooth', 'lattice', 'locfit', 'matrixStats', 'mgcv', 'mime', 'nlme', 'nnet',
  'openssl', 'Rcpp', 'RcppArmadillo', 'RCurl', 'rlang', 'rpart', 'RSQLite', 'spatial', 'survival', 'sys', 'tibble', 'utf8',
  'vctrs', 'XML'
Update all/some/none? [a/s/n]: 
a
Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/data/annotation/bin/macosx/contrib/4.1/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/data/annotation/bin/macosx/contrib/4.1/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/data/experiment/bin/macosx/contrib/4.1/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/data/experiment/bin/macosx/contrib/4.1/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/workflows/bin/macosx/contrib/4.1/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/workflows/bin/macosx/contrib/4.1/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 11573Warning: cannot open URL 'https://bioconductor.org/packages/3.14/books/bin/macosx/contrib/4.1/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 11573Warning: cannot open URL 'https://bioconductor.org/packages/3.14/books/bin/macosx/contrib/4.1/PACKAGES.gz': HTTP status was '404 Not Found'

  There are binary versions available but the source versions are later:
no
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/askpass_1.1.tgz'
Content type 'application/x-gzip' length 21566 bytes (21 KB)
==================================================
downloaded 21 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/bit_4.0.5.tgz'
Content type 'application/x-gzip' length 1243615 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/bit64_4.0.5.tgz'
Content type 'application/x-gzip' length 576409 bytes (562 KB)
==================================================
downloaded 562 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/bitops_1.0-7.tgz'
Content type 'application/x-gzip' length 29174 bytes (28 KB)
==================================================
downloaded 28 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/cachem_1.0.8.tgz'
Content type 'application/x-gzip' length 67489 bytes (65 KB)
==================================================
downloaded 65 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/class_7.3-22.tgz'
Content type 'application/x-gzip' length 96138 bytes (93 KB)
==================================================
downloaded 93 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/cli_3.6.1.tgz'
Content type 'application/x-gzip' length 1365687 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/cluster_2.1.4.tgz'
Content type 'application/x-gzip' length 616213 bytes (601 KB)
==================================================
downloaded 601 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/curl_5.0.0.tgz'
Content type 'application/x-gzip' length 759005 bytes (741 KB)
==================================================
downloaded 741 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/farver_2.1.1.tgz'
Content type 'application/x-gzip' length 1943005 bytes (1.9 MB)
==================================================
downloaded 1.9 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/fastmap_1.1.1.tgz'
Content type 'application/x-gzip' length 201256 bytes (196 KB)
==================================================
downloaded 196 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/foreign_0.8-84.tgz'
Content type 'application/x-gzip' length 331923 bytes (324 KB)
==================================================
downloaded 324 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/glue_1.6.2.tgz'
Content type 'application/x-gzip' length 151977 bytes (148 KB)
==================================================
downloaded 148 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/jsonlite_1.8.4.tgz'
Content type 'application/x-gzip' length 1113981 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/KernSmooth_2.23-21.tgz'
Content type 'application/x-gzip' length 100407 bytes (98 KB)
==================================================
downloaded 98 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/lattice_0.21-8.tgz'
Content type 'application/x-gzip' length 1349836 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/locfit_1.5-9.7.tgz'
Content type 'application/x-gzip' length 772384 bytes (754 KB)
==================================================
downloaded 754 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/matrixStats_0.63.0.tgz'
Content type 'application/x-gzip' length 592172 bytes (578 KB)
==================================================
downloaded 578 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/mgcv_1.8-42.tgz'
Content type 'application/x-gzip' length 3737078 bytes (3.6 MB)
==================================================
downloaded 3.6 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/mime_0.12.tgz'
Content type 'application/x-gzip' length 34812 bytes (33 KB)
==================================================
downloaded 33 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/nlme_3.1-162.tgz'
Content type 'application/x-gzip' length 2400717 bytes (2.3 MB)
==================================================
downloaded 2.3 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/nnet_7.3-19.tgz'
Content type 'application/x-gzip' length 129034 bytes (126 KB)
==================================================
downloaded 126 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/openssl_2.0.6.tgz'
Content type 'application/x-gzip' length 2886168 bytes (2.8 MB)
==================================================
downloaded 2.8 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/Rcpp_1.0.10.tgz'
Content type 'application/x-gzip' length 3242867 bytes (3.1 MB)
==================================================
downloaded 3.1 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/RcppArmadillo_0.12.2.0.0.tgz'
Content type 'application/x-gzip' length 1570686 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/RCurl_1.98-1.12.tgz'
Content type 'application/x-gzip' length 1089009 bytes (1.0 MB)
==================================================
downloaded 1.0 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/rlang_1.1.1.tgz'
Content type 'application/x-gzip' length 1852475 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/rpart_4.1.19.tgz'
Content type 'application/x-gzip' length 980040 bytes (957 KB)
==================================================
downloaded 957 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/RSQLite_2.3.1.tgz'
Content type 'application/x-gzip' length 4340278 bytes (4.1 MB)
==================================================
downloaded 4.1 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/spatial_7.3-16.tgz'
Content type 'application/x-gzip' length 157695 bytes (153 KB)
==================================================
downloaded 153 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/survival_3.5-5.tgz'
Content type 'application/x-gzip' length 6768208 bytes (6.5 MB)
==================================================
downloaded 6.5 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/sys_3.4.1.tgz'
Content type 'application/x-gzip' length 47312 bytes (46 KB)
==================================================
downloaded 46 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/tibble_3.2.1.tgz'
Content type 'application/x-gzip' length 676416 bytes (660 KB)
==================================================
downloaded 660 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/utf8_1.2.3.tgz'
Content type 'application/x-gzip' length 196912 bytes (192 KB)
==================================================
downloaded 192 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/vctrs_0.6.2.tgz'
Content type 'application/x-gzip' length 1850681 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/XML_3.99-0.14.tgz'
Content type 'application/x-gzip' length 1873852 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

The downloaded binary packages are in
    /var/folders/db/_9mqvxh50pb53z2xy8z_xhjr0000gn/T//RtmpXjWyRf/downloaded_packages
installing the source packages ‘boot’, ‘codetools’

trying URL 'https://cran.rstudio.com/src/contrib/boot_1.3-31.tar.gz'
Content type 'application/x-gzip' length 238458 bytes (232 KB)
==================================================
downloaded 232 KB

trying URL 'https://cran.rstudio.com/src/contrib/codetools_0.2-20.tar.gz'
Content type 'application/x-gzip' length 38683 bytes (37 KB)
==================================================
downloaded 37 KB

* installing *source* package ‘boot’ ...
** package ‘boot’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (boot)
* installing *source* package ‘codetools’ ...
** package ‘codetools’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (codetools)

The downloaded source packages are in
    ‘/private/var/folders/db/_9mqvxh50pb53z2xy8z_xhjr0000gn/T/RtmpXjWyRf/downloaded_packages’

BiocManager::install(“pheatmap”)

RNA-seq Analysis

workflow: raw counts -> normalization -> unsupervised clustering (PCA) -> DE analysis -> shrinking log2 fold change -> results exploration - can add more downstream analysis as well

BiocManager::install("pheatmap")
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for
details.
Replacement repositories:
    CRAN: https://cran.rstudio.com/
Bioconductor version 3.14 (BiocManager 1.30.26), R 4.1.3 (2022-03-10)
Installing package(s) 'pheatmap'
Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/data/annotation/bin/macosx/contrib/4.1/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/data/annotation/bin/macosx/contrib/4.1/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/data/experiment/bin/macosx/contrib/4.1/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/data/experiment/bin/macosx/contrib/4.1/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/workflows/bin/macosx/contrib/4.1/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/workflows/bin/macosx/contrib/4.1/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 11573Warning: cannot open URL 'https://bioconductor.org/packages/3.14/books/bin/macosx/contrib/4.1/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 11573Warning: cannot open URL 'https://bioconductor.org/packages/3.14/books/bin/macosx/contrib/4.1/PACKAGES.gz': HTTP status was '404 Not Found'Warning: lzma decoder corrupt data

  There is a binary version available but the source version is later:
installing the source package ‘pheatmap’

trying URL 'https://cran.rstudio.com/src/contrib/pheatmap_1.0.13.tar.gz'
Content type 'application/x-gzip' length 15162 bytes (14 KB)
==================================================
downloaded 14 KB

* installing *source* package ‘pheatmap’ ...
** package ‘pheatmap’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (pheatmap)

The downloaded source packages are in
    ‘/private/var/folders/db/_9mqvxh50pb53z2xy8z_xhjr0000gn/T/RtmpXjWyRf/downloaded_packages’
Old packages: 'askpass', 'bit', 'bit64', 'bitops', 'cachem', 'class', 'cli', 'cluster', 'curl', 'farver', 'fastmap',
  'foreign', 'glue', 'jsonlite', 'KernSmooth', 'lattice', 'locfit', 'matrixStats', 'mgcv', 'mime', 'nlme', 'nnet',
  'openssl', 'Rcpp', 'RcppArmadillo', 'RCurl', 'rlang', 'rpart', 'RSQLite', 'spatial', 'survival', 'sys', 'tibble',
  'utf8', 'vctrs', 'XML'
Update all/some/none? [a/s/n]: 
a
Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/data/annotation/bin/macosx/contrib/4.1/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/data/annotation/bin/macosx/contrib/4.1/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/data/experiment/bin/macosx/contrib/4.1/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/data/experiment/bin/macosx/contrib/4.1/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/workflows/bin/macosx/contrib/4.1/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/workflows/bin/macosx/contrib/4.1/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 11573Warning: cannot open URL 'https://bioconductor.org/packages/3.14/books/bin/macosx/contrib/4.1/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 11573Warning: cannot open URL 'https://bioconductor.org/packages/3.14/books/bin/macosx/contrib/4.1/PACKAGES.gz': HTTP status was '404 Not Found'

  There are binary versions available but the source versions are later:
no
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/askpass_1.1.tgz'
Content type 'application/x-gzip' length 21566 bytes (21 KB)
==================================================
downloaded 21 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/bit_4.0.5.tgz'
Content type 'application/x-gzip' length 1243615 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/bit64_4.0.5.tgz'
Content type 'application/x-gzip' length 576409 bytes (562 KB)
==================================================
downloaded 562 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/bitops_1.0-7.tgz'
Content type 'application/x-gzip' length 29174 bytes (28 KB)
==================================================
downloaded 28 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/cachem_1.0.8.tgz'
Content type 'application/x-gzip' length 67489 bytes (65 KB)
==================================================
downloaded 65 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/class_7.3-22.tgz'
Content type 'application/x-gzip' length 96138 bytes (93 KB)
==================================================
downloaded 93 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/cli_3.6.1.tgz'
Content type 'application/x-gzip' length 1365687 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/cluster_2.1.4.tgz'
Content type 'application/x-gzip' length 616213 bytes (601 KB)
==================================================
downloaded 601 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/curl_5.0.0.tgz'
Content type 'application/x-gzip' length 759005 bytes (741 KB)
==================================================
downloaded 741 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/farver_2.1.1.tgz'
Content type 'application/x-gzip' length 1943005 bytes (1.9 MB)
==================================================
downloaded 1.9 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/fastmap_1.1.1.tgz'
Content type 'application/x-gzip' length 201256 bytes (196 KB)
==================================================
downloaded 196 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/foreign_0.8-84.tgz'
Content type 'application/x-gzip' length 331923 bytes (324 KB)
==================================================
downloaded 324 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/glue_1.6.2.tgz'
Content type 'application/x-gzip' length 151977 bytes (148 KB)
==================================================
downloaded 148 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/jsonlite_1.8.4.tgz'
Content type 'application/x-gzip' length 1113981 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/KernSmooth_2.23-21.tgz'
Content type 'application/x-gzip' length 100407 bytes (98 KB)
==================================================
downloaded 98 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/lattice_0.21-8.tgz'
Content type 'application/x-gzip' length 1349836 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/locfit_1.5-9.7.tgz'
Content type 'application/x-gzip' length 772384 bytes (754 KB)
==================================================
downloaded 754 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/matrixStats_0.63.0.tgz'
Content type 'application/x-gzip' length 592172 bytes (578 KB)
==================================================
downloaded 578 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/mgcv_1.8-42.tgz'
Content type 'application/x-gzip' length 3737078 bytes (3.6 MB)
==================================================
downloaded 3.6 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/mime_0.12.tgz'
Content type 'application/x-gzip' length 34812 bytes (33 KB)
==================================================
downloaded 33 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/nlme_3.1-162.tgz'
Content type 'application/x-gzip' length 2400717 bytes (2.3 MB)
==================================================
downloaded 2.3 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/nnet_7.3-19.tgz'
Content type 'application/x-gzip' length 129034 bytes (126 KB)
==================================================
downloaded 126 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/openssl_2.0.6.tgz'
Content type 'application/x-gzip' length 2886168 bytes (2.8 MB)
==================================================
downloaded 2.8 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/Rcpp_1.0.10.tgz'
Content type 'application/x-gzip' length 3242867 bytes (3.1 MB)
==================================================
downloaded 3.1 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/RcppArmadillo_0.12.2.0.0.tgz'
Content type 'application/x-gzip' length 1570686 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/RCurl_1.98-1.12.tgz'
Content type 'application/x-gzip' length 1089009 bytes (1.0 MB)
==================================================
downloaded 1.0 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/rlang_1.1.1.tgz'
Content type 'application/x-gzip' length 1852475 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/rpart_4.1.19.tgz'
Content type 'application/x-gzip' length 980040 bytes (957 KB)
==================================================
downloaded 957 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/RSQLite_2.3.1.tgz'
Content type 'application/x-gzip' length 4340278 bytes (4.1 MB)
==================================================
downloaded 4.1 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/spatial_7.3-16.tgz'
Content type 'application/x-gzip' length 157695 bytes (153 KB)
==================================================
downloaded 153 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/survival_3.5-5.tgz'
Content type 'application/x-gzip' length 6768208 bytes (6.5 MB)
==================================================
downloaded 6.5 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/sys_3.4.1.tgz'
Content type 'application/x-gzip' length 47312 bytes (46 KB)
==================================================
downloaded 46 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/tibble_3.2.1.tgz'
Content type 'application/x-gzip' length 676416 bytes (660 KB)
==================================================
downloaded 660 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/utf8_1.2.3.tgz'
Content type 'application/x-gzip' length 196912 bytes (192 KB)
==================================================
downloaded 192 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/vctrs_0.6.2.tgz'
Content type 'application/x-gzip' length 1850681 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/XML_3.99-0.14.tgz'
Content type 'application/x-gzip' length 1873852 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

The downloaded binary packages are in
    /var/folders/db/_9mqvxh50pb53z2xy8z_xhjr0000gn/T//RtmpXjWyRf/downloaded_packages

#dependencies

library(DESeq2)
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval,
    evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order,
    paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
    table, tapply, union, unique, unsplit, which.max, which.min


Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

    expand.grid, I, unname

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: ‘MatrixGenerics’

The following objects are masked from ‘package:matrixStats’:

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins,
    colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs,
    colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs,
    colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans,
    colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs,
    rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats,
    rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs,
    rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: ‘Biobase’

The following object is masked from ‘package:MatrixGenerics’:

    rowMedians

The following objects are masked from ‘package:matrixStats’:

    anyMissing, rowMedians
library(pheatmap)

Preprocessing

Reading and rounding the values of raw counts file (geneid x sample names)

## Loading Input files and creating DESeq2 object
raw_counts <- read.delim("counts.txt", header = T, row.names = 1)
raw_counts <- ceiling(raw_counts) #round them up to integers
head(raw_counts)

Loading metadata

meta_data <- read.delim("sampleGroups.txt", header = T, row.names = 1)
head(meta_data)

If the row names of metadata and col names of raw counts data: idx <- match(rownames(metadata), colnames(rawcounts)) and apply the idx to the desired data to be reordered.

Modelling DeSeq2 Object

dds <- DESeqDataSetFromMatrix(countData = raw_counts,
                              colData = meta_data,
                              design = ~group) #group is the condition:resistant or sensitive in this case
converting counts to integer mode
Warning: some variables in design formula are characters, converting to factors
dds
class: DESeqDataSet 
dim: 60313 6 
metadata(1): version
assays(1): counts
rownames(60313): ENSG00000000003 ENSG00000000005 ... __not_aligned __alignment_not_unique
rowData names(0):
colnames(6): Ovcar4_sens_1 Ovcar4_sens_2 ... Ovcar4_res_2 Ovcar4_res_3
colData names(1): group

Filter out low gene counts

keep <- rowSums(counts(dds) >= 10) >= 3
dds <- dds[keep,]

counts(dds) -> gets the count matrix rowSums() -> for each gene counts the samples that are over 10

DE Analysis

dds <- DESeq(dds)
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing

Normalization and Log Transformation (transformed counts)

#estimateSizeFactors(dds)
#sizeFactors(dds)

#normalization
norm.counts <- counts(dds, normalized = TRUE) #normalize the counts for accuracy
write.csv(norm.counts, file = "normalized_counts.txt", row.names = TRUE)
head(norm.counts)
                Ovcar4_sens_1 Ovcar4_sens_2 Ovcar4_sens_3 Ovcar4_res_1 Ovcar4_res_2 Ovcar4_res_3
ENSG00000000003     1713.9751     1991.9480     2010.5017    1725.0727    1784.2223    1574.2618
ENSG00000000419     3320.7658     3089.6196     3120.6910    4280.8087    3391.3424    4674.2667
ENSG00000000457      324.4762      309.5147      340.3142     378.5549     431.2054     492.9857
ENSG00000000460     1027.9953     1204.8964     1407.3512    1197.4496     961.4120     966.9104
ENSG00000000971      855.5259     1627.1628     1416.1778    1721.1499     403.7051     610.8171
ENSG00000001036     2634.7860     2977.9733     2676.4191    3102.9733    2118.6265    2288.1813
#log transformation, transformed counts
vsd <- vst(dds, blind = FALSE) 

#creating as a matrix
vsd_matrix <- assay(vsd)
head(vsd_matrix)
                Ovcar4_sens_1 Ovcar4_sens_2 Ovcar4_sens_3 Ovcar4_res_1 Ovcar4_res_2 Ovcar4_res_3
ENSG00000000003     10.801797     11.010654     11.023574    10.810742    10.857502    10.684166
ENSG00000000419     11.728024     11.626197     11.640310    12.087585    11.757735    12.212452
ENSG00000000457      8.618568      8.562078      8.676013     8.805835     8.967180     9.135834
ENSG00000000460     10.101553     10.317121     10.529758    10.308668    10.011254    10.018929
ENSG00000000971      9.854852     10.729842     10.538351    10.807586     8.885186     9.411042
ENSG00000001036     11.402035     11.574313     11.424065    11.632279    11.096646    11.204261

Adding correlation to log transformation

vsd_cor <- cor(vsd_matrix) #applies correlation for a pheatmap
head(vsd_cor)
              Ovcar4_sens_1 Ovcar4_sens_2 Ovcar4_sens_3 Ovcar4_res_1 Ovcar4_res_2 Ovcar4_res_3
Ovcar4_sens_1     1.0000000     0.9915548     0.9882826    0.9635885    0.9558955    0.9657405
Ovcar4_sens_2     0.9915548     1.0000000     0.9955243    0.9661423    0.9481214    0.9572114
Ovcar4_sens_3     0.9882826     0.9955243     1.0000000    0.9677040    0.9477967    0.9572125
Ovcar4_res_1      0.9635885     0.9661423     0.9677040    1.0000000    0.9764804    0.9828277
Ovcar4_res_2      0.9558955     0.9481214     0.9477967    0.9764804    1.0000000    0.9845953
Ovcar4_res_3      0.9657405     0.9572114     0.9572125    0.9828277    0.9845953    1.0000000
vsd_cor <- data.frame(vsd_cor)

pheatmap(vsd_cor, annotation = select(meta_data, group))

1 indicates strong correlation - shows a good biological relevance. - Same groups have correlation of 1.

This plot supports that: - Chemo-sensitive and chemo-resistant samples have distinct gene expression profiles -> distinct transcriptomic level. - The clustering and correlation structure suggest clear biological separation, which is a good foundation for further differential expression or biomarker analysis.

Unsupervised Clustering

plotPCA(vsd, intgroup = c("group")) # does not want the matrix version

  • PC1 explains 87% of the variance — this is the main axis separating your samples.
  • Clear separation between two group -> This suggests strong transcriptomic differences between the two groups.
  • PC2 (8% variance) captures minor variation within groups.

Hierarchical Clustering

#plotting hierarchical clustering using vst transformed counts
sampleDists <- dist(t(assay(vsd)))
plot(hclust(sampleDists, method = "complete"))

Plot dispersion estimates – used DESeq2 object

mean.counts <- apply(raw_counts[,1:3],1,mean)

var.counts <- apply(raw_counts[,1:3],1,var)

plotDispEsts(dds)

Key observation:

Get DE results

dds.res <- results(dds, contrast = c("group","chemo_sensitive", "chemo_resistant"), alpha = 0.05)
summary(dds.res)

out of 18577 with nonzero total read count
adjusted p-value < 0.05
LFC > 0 (up)       : 2156, 12%
LFC < 0 (down)     : 1875, 10%
outliers [1]       : 8, 0.043%
low counts [2]     : 0, 0%
(mean count < 6)
[1] see 'cooksCutoff' argument of ?results
[2] see 'independentFiltering' argument of ?results
mcols(dds.res)$description
[1] "mean of normalized counts for all samples"                       
[2] "log2 fold change (MLE): group chemo_sensitive vs chemo_resistant"
[3] "standard error: group chemo sensitive vs chemo resistant"        
[4] "Wald statistic: group chemo sensitive vs chemo resistant"        
[5] "Wald test p-value: group chemo sensitive vs chemo resistant"     
[6] "BH adjusted p-values"                                            
write.csv(as.data.frame(dds.res), file="DE_sensitiveVSresistant_results.csv")

Summary of Differential Expression Results: - 18,577 genes had a nonzero total read count (i.e., were expressed in at least one sample). - 2,156 genes were upregulated in chemo_sensitive vs chemo_resistant (12%). - 1,875 genes were downregulated (10%). - This means ~22% of all expressed genes are significantly different between the two conditions. - 8 genes (0.043%) were flagged as outliers due to extreme values (checked using Cook’s distance). - 0 genes were filtered out due to low mean counts (<6), likely because of independent filtering.

plotMA(dds.res)

  • LFC > 0 is up-regulated genes; LFC < 0 is down-regulated genes.
  • Grey points are the genes that are not statistically significant.
  • Blue points genes with p.adj < 0.05 (significantly differentially expressed)
  • There is a large number of significantly differentially expressed genes, especially in genes with moderate-to-high expression (middle x-axis).
  • The triangle markers suggest some genes have very large fold changes and may be biologically interesting.

Volcano Plot

BiocManager::install('EnhancedVolcano')
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")'
for details.
Replacement repositories:
    CRAN: https://cran.rstudio.com/
Bioconductor version 3.14 (BiocManager 1.30.26), R 4.1.3 (2022-03-10)
Installing package(s) 'EnhancedVolcano'
also installing the dependencies ‘fs’, ‘rappdirs’, ‘sass’, ‘evaluate’, ‘highr’, ‘xfun’, ‘bslib’, ‘fontawesome’, ‘jquerylib’, ‘tinytex’, ‘knitr’, ‘rmarkdown’, ‘yaml’, ‘stringr’, ‘vctrs’, ‘later’, ‘stringi’, ‘extrafontdb’, ‘Rttf2pt1’, ‘digest’, ‘base64enc’, ‘htmltools’, ‘htmlwidgets’, ‘tidyr’, ‘lazyeval’, ‘crosstalk’, ‘purrr’, ‘data.table’, ‘promises’, ‘beeswarm’, ‘vipor’, ‘systemfonts’, ‘textshaping’, ‘proj4’, ‘ash’, ‘maps’, ‘extrafont’, ‘plotly’, ‘Cairo’, ‘ggbeeswarm’, ‘ragg’, ‘ggrepel’, ‘ggalt’, ‘ggrastr’

Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/data/annotation/bin/macosx/contrib/4.1/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/data/annotation/bin/macosx/contrib/4.1/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/data/experiment/bin/macosx/contrib/4.1/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/data/experiment/bin/macosx/contrib/4.1/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/workflows/bin/macosx/contrib/4.1/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/workflows/bin/macosx/contrib/4.1/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 11573Warning: cannot open URL 'https://bioconductor.org/packages/3.14/books/bin/macosx/contrib/4.1/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 11573Warning: cannot open URL 'https://bioconductor.org/packages/3.14/books/bin/macosx/contrib/4.1/PACKAGES.gz': HTTP status was '404 Not Found'

  There are binary versions available but the source versions are later:
no
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/fs_1.6.2.tgz'
Content type 'application/x-gzip' length 569071 bytes (555 KB)
==================================================
downloaded 555 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/rappdirs_0.3.3.tgz'
Content type 'application/x-gzip' length 45686 bytes (44 KB)
==================================================
downloaded 44 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/sass_0.4.6.tgz'
Content type 'application/x-gzip' length 2392703 bytes (2.3 MB)
==================================================
downloaded 2.3 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/xfun_0.39.tgz'
Content type 'application/x-gzip' length 430615 bytes (420 KB)
==================================================
downloaded 420 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/jquerylib_0.1.4.tgz'
Content type 'application/x-gzip' length 525978 bytes (513 KB)
==================================================
downloaded 513 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/yaml_2.3.7.tgz'
Content type 'application/x-gzip' length 204951 bytes (200 KB)
==================================================
downloaded 200 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/vctrs_0.6.2.tgz'
Content type 'application/x-gzip' length 1850681 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/later_1.3.1.tgz'
Content type 'application/x-gzip' length 612981 bytes (598 KB)
==================================================
downloaded 598 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/stringi_1.7.12.tgz'
Content type 'application/x-gzip' length 14448461 bytes (13.8 MB)
==================================================
downloaded 13.8 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/extrafontdb_1.0.tgz'
Content type 'application/x-gzip' length 6792 bytes
==================================================
downloaded 6792 bytes

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/Rttf2pt1_1.3.12.tgz'
Content type 'application/x-gzip' length 106495 bytes (103 KB)
==================================================
downloaded 103 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/digest_0.6.31.tgz'
Content type 'application/x-gzip' length 298704 bytes (291 KB)
==================================================
downloaded 291 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/base64enc_0.1-3.tgz'
Content type 'application/x-gzip' length 31642 bytes (30 KB)
==================================================
downloaded 30 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/htmltools_0.5.5.tgz'
Content type 'application/x-gzip' length 346776 bytes (338 KB)
==================================================
downloaded 338 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/tidyr_1.3.0.tgz'
Content type 'application/x-gzip' length 1324625 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/lazyeval_0.2.2.tgz'
Content type 'application/x-gzip' length 156515 bytes (152 KB)
==================================================
downloaded 152 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/purrr_1.0.1.tgz'
Content type 'application/x-gzip' length 509931 bytes (497 KB)
==================================================
downloaded 497 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/data.table_1.14.8.tgz'
Content type 'application/x-gzip' length 2376122 bytes (2.3 MB)
==================================================
downloaded 2.3 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/promises_1.2.0.1.tgz'
Content type 'application/x-gzip' length 1782018 bytes (1.7 MB)
==================================================
downloaded 1.7 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/beeswarm_0.4.0.tgz'
Content type 'application/x-gzip' length 81533 bytes (79 KB)
==================================================
downloaded 79 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/systemfonts_1.0.4.tgz'
Content type 'application/x-gzip' length 5900454 bytes (5.6 MB)
==================================================
downloaded 5.6 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/textshaping_0.3.6.tgz'
Content type 'application/x-gzip' length 1291817 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/proj4_1.0-12.tgz'
Content type 'application/x-gzip' length 17782645 bytes (17.0 MB)
==================================================
downloaded 17.0 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/ash_1.0-15.tgz'
Content type 'application/x-gzip' length 29954 bytes (29 KB)
==================================================
downloaded 29 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/maps_3.4.1.tgz'
Content type 'application/x-gzip' length 3105432 bytes (3.0 MB)
==================================================
downloaded 3.0 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/extrafont_0.19.tgz'
Content type 'application/x-gzip' length 54318 bytes (53 KB)
==================================================
downloaded 53 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/Cairo_1.6-0.tgz'
Content type 'application/x-gzip' length 22861382 bytes (21.8 MB)
==================================================
downloaded 21.8 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/ggbeeswarm_0.7.2.tgz'
Content type 'application/x-gzip' length 1756363 bytes (1.7 MB)
==================================================
downloaded 1.7 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/ragg_1.2.5.tgz'
Content type 'application/x-gzip' length 9223518 bytes (8.8 MB)
==================================================
downloaded 8.8 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/ggrepel_0.9.3.tgz'
Content type 'application/x-gzip' length 577454 bytes (563 KB)
==================================================
downloaded 563 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/ggalt_0.4.0.tgz'
Content type 'application/x-gzip' length 2361598 bytes (2.3 MB)
==================================================
downloaded 2.3 MB

trying URL 'https://bioconductor.org/packages/3.14/bioc/bin/macosx/contrib/4.1/EnhancedVolcano_1.12.0.tgz'
Content type 'application/octet-stream' length 5045617 bytes (4.8 MB)
==================================================
downloaded 4.8 MB

The downloaded binary packages are in
    /var/folders/db/_9mqvxh50pb53z2xy8z_xhjr0000gn/T//RtmpapzpFa/downloaded_packages
installing the source packages ‘evaluate’, ‘highr’, ‘bslib’, ‘fontawesome’, ‘tinytex’, ‘knitr’, ‘rmarkdown’, ‘stringr’, ‘htmlwidgets’, ‘crosstalk’, ‘vipor’, ‘plotly’, ‘ggrastr’

trying URL 'https://cran.rstudio.com/src/contrib/evaluate_1.0.4.tar.gz'
Content type 'application/x-gzip' length 39226 bytes (38 KB)
==================================================
downloaded 38 KB

trying URL 'https://cran.rstudio.com/src/contrib/highr_0.11.tar.gz'
Content type 'application/x-gzip' length 13851 bytes (13 KB)
==================================================
downloaded 13 KB

trying URL 'https://cran.rstudio.com/src/contrib/bslib_0.9.0.tar.gz'
Content type 'application/x-gzip' length 5428353 bytes (5.2 MB)
==================================================
downloaded 5.2 MB

trying URL 'https://cran.rstudio.com/src/contrib/fontawesome_0.5.3.tar.gz'
Content type 'application/x-gzip' length 1320479 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

trying URL 'https://cran.rstudio.com/src/contrib/tinytex_0.57.tar.gz'
Content type 'application/x-gzip' length 36295 bytes (35 KB)
==================================================
downloaded 35 KB

trying URL 'https://cran.rstudio.com/src/contrib/knitr_1.50.tar.gz'
Content type 'application/x-gzip' length 534264 bytes (521 KB)
==================================================
downloaded 521 KB

trying URL 'https://cran.rstudio.com/src/contrib/rmarkdown_2.29.tar.gz'
Content type 'application/x-gzip' length 2194660 bytes (2.1 MB)
==================================================
downloaded 2.1 MB

trying URL 'https://cran.rstudio.com/src/contrib/stringr_1.5.1.tar.gz'
Content type 'application/x-gzip' length 176599 bytes (172 KB)
==================================================
downloaded 172 KB

trying URL 'https://cran.rstudio.com/src/contrib/htmlwidgets_1.6.4.tar.gz'
Content type 'application/x-gzip' length 868895 bytes (848 KB)
==================================================
downloaded 848 KB

trying URL 'https://cran.rstudio.com/src/contrib/crosstalk_1.2.1.tar.gz'
Content type 'application/x-gzip' length 297970 bytes (290 KB)
==================================================
downloaded 290 KB

trying URL 'https://cran.rstudio.com/src/contrib/vipor_0.4.7.tar.gz'
Content type 'application/x-gzip' length 4688496 bytes (4.5 MB)
==================================================
downloaded 4.5 MB

trying URL 'https://cran.rstudio.com/src/contrib/plotly_4.11.0.tar.gz'
Content type 'application/x-gzip' length 4681790 bytes (4.5 MB)
==================================================
downloaded 4.5 MB

trying URL 'https://cran.rstudio.com/src/contrib/ggrastr_1.0.2.tar.gz'
Content type 'application/x-gzip' length 2592994 bytes (2.5 MB)
==================================================
downloaded 2.5 MB

* installing *source* package ‘evaluate’ ...
** package ‘evaluate’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (evaluate)
* installing *source* package ‘highr’ ...
** package ‘highr’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (highr)
* installing *source* package ‘bslib’ ...
** package ‘bslib’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  namespace ‘htmltools’ 0.5.5 is being loaded, but >= 0.5.8 is required
Calls: <Anonymous> ... withCallingHandlers -> loadNamespace -> namespaceImport -> loadNamespace
Execution halted
ERROR: lazy loading failed for package ‘bslib’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/bslib’
Warning: installation of package ‘bslib’ had non-zero exit status* installing *source* package ‘fontawesome’ ...
** package ‘fontawesome’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (fontawesome)
* installing *source* package ‘tinytex’ ...
** package ‘tinytex’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  namespace ‘xfun’ 0.39 is being loaded, but >= 0.48 is required
Calls: <Anonymous> ... namespaceImportFrom -> asNamespace -> loadNamespace
Execution halted
ERROR: lazy loading failed for package ‘tinytex’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/tinytex’
Warning: installation of package ‘tinytex’ had non-zero exit status* installing *source* package ‘stringr’ ...
** package ‘stringr’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (stringr)
* installing *source* package ‘crosstalk’ ...
** package ‘crosstalk’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (crosstalk)
* installing *source* package ‘vipor’ ...
** package ‘vipor’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (vipor)
* installing *source* package ‘ggrastr’ ...
** package ‘ggrastr’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ggrastr)
* installing *source* package ‘knitr’ ...
** package ‘knitr’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  namespace ‘xfun’ 0.39 is being loaded, but >= 0.51 is required
Calls: <Anonymous> ... namespaceImportFrom -> asNamespace -> loadNamespace
Execution halted
ERROR: lazy loading failed for package ‘knitr’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/knitr’
Warning: installation of package ‘knitr’ had non-zero exit statusERROR: dependencies ‘bslib’, ‘knitr’, ‘tinytex’ are not available for package ‘rmarkdown’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/rmarkdown’
Warning: installation of package ‘rmarkdown’ had non-zero exit statusERROR: dependencies ‘knitr’, ‘rmarkdown’ are not available for package ‘htmlwidgets’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/htmlwidgets’
Warning: installation of package ‘htmlwidgets’ had non-zero exit statusERROR: dependency ‘htmlwidgets’ is not available for package ‘plotly’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/plotly’
Warning: installation of package ‘plotly’ had non-zero exit status
The downloaded source packages are in
    ‘/private/var/folders/db/_9mqvxh50pb53z2xy8z_xhjr0000gn/T/RtmpapzpFa/downloaded_packages’
Old packages: 'askpass', 'bit', 'bit64', 'bitops', 'cachem', 'Cairo', 'class', 'cli', 'cluster', 'curl', 'data.table',
  'digest', 'dplyr', 'farver', 'fastmap', 'foreign', 'fs', 'ggrepel', 'glue', 'htmltools', 'jsonlite', 'KernSmooth',
  'later', 'lattice', 'locfit', 'maps', 'matrixStats', 'mgcv', 'mime', 'nlme', 'nnet', 'openssl', 'proj4', 'promises',
  'purrr', 'ragg', 'Rcpp', 'RcppArmadillo', 'RCurl', 'rlang', 'rpart', 'RSQLite', 'sass', 'spatial', 'stringi',
  'survival', 'sys', 'systemfonts', 'textshaping', 'tibble', 'tidyr', 'tidyselect', 'utf8', 'vctrs', 'xfun', 'XML',
  'yaml'
Update all/some/none? [a/s/n]: 
a
Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/data/annotation/bin/macosx/contrib/4.1/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/data/annotation/bin/macosx/contrib/4.1/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/data/experiment/bin/macosx/contrib/4.1/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/data/experiment/bin/macosx/contrib/4.1/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/workflows/bin/macosx/contrib/4.1/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/workflows/bin/macosx/contrib/4.1/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 11573Warning: cannot open URL 'https://bioconductor.org/packages/3.14/books/bin/macosx/contrib/4.1/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 11573Warning: cannot open URL 'https://bioconductor.org/packages/3.14/books/bin/macosx/contrib/4.1/PACKAGES.gz': HTTP status was '404 Not Found'

  There are binary versions available but the source versions are later:
no
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/askpass_1.1.tgz'
Content type 'application/x-gzip' length 21566 bytes (21 KB)
==================================================
downloaded 21 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/bit_4.0.5.tgz'
Content type 'application/x-gzip' length 1243615 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/bit64_4.0.5.tgz'
Content type 'application/x-gzip' length 576409 bytes (562 KB)
==================================================
downloaded 562 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/bitops_1.0-7.tgz'
Content type 'application/x-gzip' length 29174 bytes (28 KB)
==================================================
downloaded 28 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/cachem_1.0.8.tgz'
Content type 'application/x-gzip' length 67489 bytes (65 KB)
==================================================
downloaded 65 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/Cairo_1.6-0.tgz'
Content type 'application/x-gzip' length 22861382 bytes (21.8 MB)
==================================================
downloaded 21.8 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/class_7.3-22.tgz'
Content type 'application/x-gzip' length 96138 bytes (93 KB)
==================================================
downloaded 93 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/cli_3.6.1.tgz'
Content type 'application/x-gzip' length 1365687 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/cluster_2.1.4.tgz'
Content type 'application/x-gzip' length 616213 bytes (601 KB)
==================================================
downloaded 601 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/curl_5.0.0.tgz'
Content type 'application/x-gzip' length 759005 bytes (741 KB)
==================================================
downloaded 741 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/data.table_1.14.8.tgz'
Content type 'application/x-gzip' length 2376122 bytes (2.3 MB)
==================================================
downloaded 2.3 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/digest_0.6.31.tgz'
Content type 'application/x-gzip' length 298704 bytes (291 KB)
==================================================
downloaded 291 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/dplyr_1.1.2.tgz'
Content type 'application/x-gzip' length 1561346 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/farver_2.1.1.tgz'
Content type 'application/x-gzip' length 1943005 bytes (1.9 MB)
==================================================
downloaded 1.9 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/fastmap_1.1.1.tgz'
Content type 'application/x-gzip' length 201256 bytes (196 KB)
==================================================
downloaded 196 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/foreign_0.8-84.tgz'
Content type 'application/x-gzip' length 331923 bytes (324 KB)
==================================================
downloaded 324 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/fs_1.6.2.tgz'
Content type 'application/x-gzip' length 569071 bytes (555 KB)
==================================================
downloaded 555 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/ggrepel_0.9.3.tgz'
Content type 'application/x-gzip' length 577454 bytes (563 KB)
==================================================
downloaded 563 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/glue_1.6.2.tgz'
Content type 'application/x-gzip' length 151977 bytes (148 KB)
==================================================
downloaded 148 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/htmltools_0.5.5.tgz'
Content type 'application/x-gzip' length 346776 bytes (338 KB)
==================================================
downloaded 338 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/jsonlite_1.8.4.tgz'
Content type 'application/x-gzip' length 1113981 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/KernSmooth_2.23-21.tgz'
Content type 'application/x-gzip' length 100407 bytes (98 KB)
==================================================
downloaded 98 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/later_1.3.1.tgz'
Content type 'application/x-gzip' length 612981 bytes (598 KB)
==================================================
downloaded 598 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/lattice_0.21-8.tgz'
Content type 'application/x-gzip' length 1349836 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/locfit_1.5-9.7.tgz'
Content type 'application/x-gzip' length 772384 bytes (754 KB)
==================================================
downloaded 754 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/maps_3.4.1.tgz'
Content type 'application/x-gzip' length 3105432 bytes (3.0 MB)
==================================================
downloaded 3.0 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/matrixStats_0.63.0.tgz'
Content type 'application/x-gzip' length 592172 bytes (578 KB)
==================================================
downloaded 578 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/mgcv_1.8-42.tgz'
Content type 'application/x-gzip' length 3737078 bytes (3.6 MB)
==================================================
downloaded 3.6 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/mime_0.12.tgz'
Content type 'application/x-gzip' length 34812 bytes (33 KB)
==================================================
downloaded 33 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/nlme_3.1-162.tgz'
Content type 'application/x-gzip' length 2400717 bytes (2.3 MB)
==================================================
downloaded 2.3 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/nnet_7.3-19.tgz'
Content type 'application/x-gzip' length 129034 bytes (126 KB)
==================================================
downloaded 126 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/openssl_2.0.6.tgz'
Content type 'application/x-gzip' length 2886168 bytes (2.8 MB)
==================================================
downloaded 2.8 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/proj4_1.0-12.tgz'
Content type 'application/x-gzip' length 17782645 bytes (17.0 MB)
==================================================
downloaded 17.0 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/promises_1.2.0.1.tgz'
Content type 'application/x-gzip' length 1782018 bytes (1.7 MB)
==================================================
downloaded 1.7 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/purrr_1.0.1.tgz'
Content type 'application/x-gzip' length 509931 bytes (497 KB)
==================================================
downloaded 497 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/ragg_1.2.5.tgz'
Content type 'application/x-gzip' length 9223518 bytes (8.8 MB)
==================================================
downloaded 8.8 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/Rcpp_1.0.10.tgz'
Content type 'application/x-gzip' length 3242867 bytes (3.1 MB)
==================================================
downloaded 3.1 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/RcppArmadillo_0.12.2.0.0.tgz'
Content type 'application/x-gzip' length 1570686 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/RCurl_1.98-1.12.tgz'
Content type 'application/x-gzip' length 1089009 bytes (1.0 MB)
==================================================
downloaded 1.0 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/rlang_1.1.1.tgz'
Content type 'application/x-gzip' length 1852475 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/rpart_4.1.19.tgz'
Content type 'application/x-gzip' length 980040 bytes (957 KB)
==================================================
downloaded 957 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/RSQLite_2.3.1.tgz'
Content type 'application/x-gzip' length 4340278 bytes (4.1 MB)
==================================================
downloaded 4.1 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/sass_0.4.6.tgz'
Content type 'application/x-gzip' length 2392703 bytes (2.3 MB)
==================================================
downloaded 2.3 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/spatial_7.3-16.tgz'
Content type 'application/x-gzip' length 157695 bytes (153 KB)
==================================================
downloaded 153 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/stringi_1.7.12.tgz'
Content type 'application/x-gzip' length 14448461 bytes (13.8 MB)
==================================================
downloaded 13.8 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/survival_3.5-5.tgz'
Content type 'application/x-gzip' length 6768208 bytes (6.5 MB)
==================================================
downloaded 6.5 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/sys_3.4.1.tgz'
Content type 'application/x-gzip' length 47312 bytes (46 KB)
==================================================
downloaded 46 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/systemfonts_1.0.4.tgz'
Content type 'application/x-gzip' length 5900454 bytes (5.6 MB)
==================================================
downloaded 5.6 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/textshaping_0.3.6.tgz'
Content type 'application/x-gzip' length 1291817 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/tibble_3.2.1.tgz'
Content type 'application/x-gzip' length 676416 bytes (660 KB)
==================================================
downloaded 660 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/tidyr_1.3.0.tgz'
Content type 'application/x-gzip' length 1324625 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/tidyselect_1.2.0.tgz'
Content type 'application/x-gzip' length 219384 bytes (214 KB)
==================================================
downloaded 214 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/utf8_1.2.3.tgz'
Content type 'application/x-gzip' length 196912 bytes (192 KB)
==================================================
downloaded 192 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/vctrs_0.6.2.tgz'
Content type 'application/x-gzip' length 1850681 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/xfun_0.39.tgz'
Content type 'application/x-gzip' length 430615 bytes (420 KB)
==================================================
downloaded 420 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/XML_3.99-0.14.tgz'
Content type 'application/x-gzip' length 1873852 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/yaml_2.3.7.tgz'
Content type 'application/x-gzip' length 204951 bytes (200 KB)
==================================================
downloaded 200 KB

The downloaded binary packages are in
    /var/folders/db/_9mqvxh50pb53z2xy8z_xhjr0000gn/T//RtmpapzpFa/downloaded_packages
library(EnhancedVolcano)
Loading required package: ggplot2

Attaching package: ‘ggplot2’

The following object is masked from ‘package:dplyr’:

    vars

Loading required package: ggrepel
Registered S3 methods overwritten by 'ggalt':
  method                  from   
  grid.draw.absoluteGrob  ggplot2
  grobHeight.absoluteGrob ggplot2
  grobWidth.absoluteGrob  ggplot2
  grobX.absoluteGrob      ggplot2
  grobY.absoluteGrob      ggplot2
EnhancedVolcano(dds.res,
    lab = rownames(dds.res),
    x = 'log2FoldChange',
    y = 'padj')

  • genes to the right are up-regulated due to LFC > 0
  • genes to the left are down-regulated due to LFC < 0
  • higher values are more statisticaly significant
  • There are many red points, meaning a large number of genes show both statistically significant changes and large expression differences between the two conditions.
  • The volcano plot confirms the biological distinction between chemo-sensitive and resistant samples.
  • Genes near the center LFC~0 are not statistically significant.

Most significant DE genes

plotCounts(dds, gene=which.min(dds.res$padj), intgroup="group")

Visualizing expression data with a heatmap

# thresholding for significanlty differentially expressed genes with at least two-ford change in expression
de.sign <- subset(dds.res, padj < 0.05 & abs(log2FoldChange) > 1)

# creating a vector of Ensembl id for those genes
de.sign.genes <- rownames(de.sign)

# subseting the vsd matrix to include only the de.sign.genes and scaling it by row so that we plot on the heatmap
scale.dat <- t(scale(t(assay(vsd)[de.sign.genes,])))
pheatmap(scale.dat[de.sign.genes,], cluster_rows=TRUE, show_rownames=FALSE, cluster_cols=TRUE)

Annotating DE Results

BiocManager::install('AnnotationDbi')
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")'
for details.
Replacement repositories:
    CRAN: https://cran.rstudio.com/
Bioconductor version 3.14 (BiocManager 1.30.26), R 4.1.3 (2022-03-10)
Warning: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install:
  'AnnotationDbi'Old packages: 'askpass', 'bit', 'bit64', 'bitops', 'cachem', 'Cairo', 'class', 'cli', 'cluster', 'curl', 'data.table',
  'digest', 'dplyr', 'farver', 'fastmap', 'foreign', 'fs', 'ggrepel', 'glue', 'htmltools', 'jsonlite', 'KernSmooth',
  'later', 'lattice', 'locfit', 'maps', 'matrixStats', 'mgcv', 'mime', 'nlme', 'nnet', 'openssl', 'proj4', 'promises',
  'purrr', 'ragg', 'Rcpp', 'RcppArmadillo', 'RCurl', 'rlang', 'rpart', 'RSQLite', 'sass', 'spatial', 'stringi',
  'survival', 'sys', 'systemfonts', 'textshaping', 'tibble', 'tidyr', 'tidyselect', 'utf8', 'vctrs', 'xfun', 'XML',
  'yaml'
Update all/some/none? [a/s/n]: 
a
Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/data/annotation/bin/macosx/contrib/4.1/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/data/annotation/bin/macosx/contrib/4.1/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/data/experiment/bin/macosx/contrib/4.1/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/data/experiment/bin/macosx/contrib/4.1/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/workflows/bin/macosx/contrib/4.1/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/workflows/bin/macosx/contrib/4.1/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 11573Warning: cannot open URL 'https://bioconductor.org/packages/3.14/books/bin/macosx/contrib/4.1/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 11573Warning: cannot open URL 'https://bioconductor.org/packages/3.14/books/bin/macosx/contrib/4.1/PACKAGES.gz': HTTP status was '404 Not Found'

  There are binary versions available but the source versions are later:
no
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/askpass_1.1.tgz'
Content type 'application/x-gzip' length 21566 bytes (21 KB)
==================================================
downloaded 21 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/bit_4.0.5.tgz'
Content type 'application/x-gzip' length 1243615 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/bit64_4.0.5.tgz'
Content type 'application/x-gzip' length 576409 bytes (562 KB)
==================================================
downloaded 562 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/bitops_1.0-7.tgz'
Content type 'application/x-gzip' length 29174 bytes (28 KB)
==================================================
downloaded 28 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/cachem_1.0.8.tgz'
Content type 'application/x-gzip' length 67489 bytes (65 KB)
==================================================
downloaded 65 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/Cairo_1.6-0.tgz'
Content type 'application/x-gzip' length 22861382 bytes (21.8 MB)
==================================================
downloaded 21.8 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/class_7.3-22.tgz'
Content type 'application/x-gzip' length 96138 bytes (93 KB)
==================================================
downloaded 93 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/cli_3.6.1.tgz'
Content type 'application/x-gzip' length 1365687 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/cluster_2.1.4.tgz'
Content type 'application/x-gzip' length 616213 bytes (601 KB)
==================================================
downloaded 601 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/curl_5.0.0.tgz'
Content type 'application/x-gzip' length 759005 bytes (741 KB)
==================================================
downloaded 741 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/data.table_1.14.8.tgz'
Content type 'application/x-gzip' length 2376122 bytes (2.3 MB)
==================================================
downloaded 2.3 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/digest_0.6.31.tgz'
Content type 'application/x-gzip' length 298704 bytes (291 KB)
==================================================
downloaded 291 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/dplyr_1.1.2.tgz'
Content type 'application/x-gzip' length 1561346 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/farver_2.1.1.tgz'
Content type 'application/x-gzip' length 1943005 bytes (1.9 MB)
==================================================
downloaded 1.9 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/fastmap_1.1.1.tgz'
Content type 'application/x-gzip' length 201256 bytes (196 KB)
==================================================
downloaded 196 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/foreign_0.8-84.tgz'
Content type 'application/x-gzip' length 331923 bytes (324 KB)
==================================================
downloaded 324 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/fs_1.6.2.tgz'
Content type 'application/x-gzip' length 569071 bytes (555 KB)
==================================================
downloaded 555 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/ggrepel_0.9.3.tgz'
Content type 'application/x-gzip' length 577454 bytes (563 KB)
==================================================
downloaded 563 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/glue_1.6.2.tgz'
Content type 'application/x-gzip' length 151977 bytes (148 KB)
==================================================
downloaded 148 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/htmltools_0.5.5.tgz'
Content type 'application/x-gzip' length 346776 bytes (338 KB)
==================================================
downloaded 338 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/jsonlite_1.8.4.tgz'
Content type 'application/x-gzip' length 1113981 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/KernSmooth_2.23-21.tgz'
Content type 'application/x-gzip' length 100407 bytes (98 KB)
==================================================
downloaded 98 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/later_1.3.1.tgz'
Content type 'application/x-gzip' length 612981 bytes (598 KB)
==================================================
downloaded 598 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/lattice_0.21-8.tgz'
Content type 'application/x-gzip' length 1349836 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/locfit_1.5-9.7.tgz'
Content type 'application/x-gzip' length 772384 bytes (754 KB)
==================================================
downloaded 754 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/maps_3.4.1.tgz'
Content type 'application/x-gzip' length 3105432 bytes (3.0 MB)
==================================================
downloaded 3.0 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/matrixStats_0.63.0.tgz'
Content type 'application/x-gzip' length 592172 bytes (578 KB)
==================================================
downloaded 578 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/mgcv_1.8-42.tgz'
Content type 'application/x-gzip' length 3737078 bytes (3.6 MB)
==================================================
downloaded 3.6 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/mime_0.12.tgz'
Content type 'application/x-gzip' length 34812 bytes (33 KB)
==================================================
downloaded 33 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/nlme_3.1-162.tgz'
Content type 'application/x-gzip' length 2400717 bytes (2.3 MB)
==================================================
downloaded 2.3 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/nnet_7.3-19.tgz'
Content type 'application/x-gzip' length 129034 bytes (126 KB)
==================================================
downloaded 126 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/openssl_2.0.6.tgz'
Content type 'application/x-gzip' length 2886168 bytes (2.8 MB)
==================================================
downloaded 2.8 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/proj4_1.0-12.tgz'
Content type 'application/x-gzip' length 17782645 bytes (17.0 MB)
==================================================
downloaded 17.0 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/promises_1.2.0.1.tgz'
Content type 'application/x-gzip' length 1782018 bytes (1.7 MB)
==================================================
downloaded 1.7 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/purrr_1.0.1.tgz'
Content type 'application/x-gzip' length 509931 bytes (497 KB)
==================================================
downloaded 497 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/ragg_1.2.5.tgz'
Content type 'application/x-gzip' length 9223518 bytes (8.8 MB)
==================================================
downloaded 8.8 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/Rcpp_1.0.10.tgz'
Content type 'application/x-gzip' length 3242867 bytes (3.1 MB)
==================================================
downloaded 3.1 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/RcppArmadillo_0.12.2.0.0.tgz'
Content type 'application/x-gzip' length 1570686 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/RCurl_1.98-1.12.tgz'
Content type 'application/x-gzip' length 1089009 bytes (1.0 MB)
==================================================
downloaded 1.0 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/rlang_1.1.1.tgz'
Content type 'application/x-gzip' length 1852475 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/rpart_4.1.19.tgz'
Content type 'application/x-gzip' length 980040 bytes (957 KB)
==================================================
downloaded 957 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/RSQLite_2.3.1.tgz'
Content type 'application/x-gzip' length 4340278 bytes (4.1 MB)
==================================================
downloaded 4.1 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/sass_0.4.6.tgz'
Content type 'application/x-gzip' length 2392703 bytes (2.3 MB)
==================================================
downloaded 2.3 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/spatial_7.3-16.tgz'
Content type 'application/x-gzip' length 157695 bytes (153 KB)
==================================================
downloaded 153 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/stringi_1.7.12.tgz'
Content type 'application/x-gzip' length 14448461 bytes (13.8 MB)
==================================================
downloaded 13.8 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/survival_3.5-5.tgz'
Content type 'application/x-gzip' length 6768208 bytes (6.5 MB)
==================================================
downloaded 6.5 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/sys_3.4.1.tgz'
Content type 'application/x-gzip' length 47312 bytes (46 KB)
==================================================
downloaded 46 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/systemfonts_1.0.4.tgz'
Content type 'application/x-gzip' length 5900454 bytes (5.6 MB)
==================================================
downloaded 5.6 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/textshaping_0.3.6.tgz'
Content type 'application/x-gzip' length 1291817 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/tibble_3.2.1.tgz'
Content type 'application/x-gzip' length 676416 bytes (660 KB)
==================================================
downloaded 660 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/tidyr_1.3.0.tgz'
Content type 'application/x-gzip' length 1324625 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/tidyselect_1.2.0.tgz'
Content type 'application/x-gzip' length 219384 bytes (214 KB)
==================================================
downloaded 214 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/utf8_1.2.3.tgz'
Content type 'application/x-gzip' length 196912 bytes (192 KB)
==================================================
downloaded 192 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/vctrs_0.6.2.tgz'
Content type 'application/x-gzip' length 1850681 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/xfun_0.39.tgz'
Content type 'application/x-gzip' length 430615 bytes (420 KB)
==================================================
downloaded 420 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/XML_3.99-0.14.tgz'
Content type 'application/x-gzip' length 1873852 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/yaml_2.3.7.tgz'
Content type 'application/x-gzip' length 204951 bytes (200 KB)
==================================================
downloaded 200 KB

The downloaded binary packages are in
    /var/folders/db/_9mqvxh50pb53z2xy8z_xhjr0000gn/T//RtmpapzpFa/downloaded_packages
BiocManager::install("org.Hs.eg.db")
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")'
for details.
Replacement repositories:
    CRAN: https://cran.rstudio.com/
Bioconductor version 3.14 (BiocManager 1.30.26), R 4.1.3 (2022-03-10)
Installing package(s) 'org.Hs.eg.db'
Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/data/annotation/bin/macosx/contrib/4.1/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/data/annotation/bin/macosx/contrib/4.1/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/data/experiment/bin/macosx/contrib/4.1/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/data/experiment/bin/macosx/contrib/4.1/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/workflows/bin/macosx/contrib/4.1/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/workflows/bin/macosx/contrib/4.1/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 11573Warning: cannot open URL 'https://bioconductor.org/packages/3.14/books/bin/macosx/contrib/4.1/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 11573Warning: cannot open URL 'https://bioconductor.org/packages/3.14/books/bin/macosx/contrib/4.1/PACKAGES.gz': HTTP status was '404 Not Found'installing the source package ‘org.Hs.eg.db’

trying URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/org.Hs.eg.db_3.14.0.tar.gz'
Content type 'application/octet-stream' length 82195112 bytes (78.4 MB)
==================================================
downloaded 78.4 MB

* installing *source* package ‘org.Hs.eg.db’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (org.Hs.eg.db)

The downloaded source packages are in
    ‘/private/var/folders/db/_9mqvxh50pb53z2xy8z_xhjr0000gn/T/RtmpapzpFa/downloaded_packages’
Old packages: 'askpass', 'bit', 'bit64', 'bitops', 'cachem', 'Cairo', 'class', 'cli', 'cluster', 'curl', 'data.table',
  'digest', 'dplyr', 'farver', 'fastmap', 'foreign', 'fs', 'ggrepel', 'glue', 'htmltools', 'jsonlite', 'KernSmooth',
  'later', 'lattice', 'locfit', 'maps', 'matrixStats', 'mgcv', 'mime', 'nlme', 'nnet', 'openssl', 'proj4', 'promises',
  'purrr', 'ragg', 'Rcpp', 'RcppArmadillo', 'RCurl', 'rlang', 'rpart', 'RSQLite', 'sass', 'spatial', 'stringi',
  'survival', 'sys', 'systemfonts', 'textshaping', 'tibble', 'tidyr', 'tidyselect', 'utf8', 'vctrs', 'xfun', 'XML',
  'yaml'
Update all/some/none? [a/s/n]: 
a
Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/data/annotation/bin/macosx/contrib/4.1/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/data/annotation/bin/macosx/contrib/4.1/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/data/experiment/bin/macosx/contrib/4.1/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/data/experiment/bin/macosx/contrib/4.1/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/workflows/bin/macosx/contrib/4.1/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.14/workflows/bin/macosx/contrib/4.1/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 11573Warning: cannot open URL 'https://bioconductor.org/packages/3.14/books/bin/macosx/contrib/4.1/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 11573Warning: cannot open URL 'https://bioconductor.org/packages/3.14/books/bin/macosx/contrib/4.1/PACKAGES.gz': HTTP status was '404 Not Found'

  There are binary versions available but the source versions are later:
no
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/askpass_1.1.tgz'
Content type 'application/x-gzip' length 21566 bytes (21 KB)
==================================================
downloaded 21 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/bit_4.0.5.tgz'
Content type 'application/x-gzip' length 1243615 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/bit64_4.0.5.tgz'
Content type 'application/x-gzip' length 576409 bytes (562 KB)
==================================================
downloaded 562 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/bitops_1.0-7.tgz'
Content type 'application/x-gzip' length 29174 bytes (28 KB)
==================================================
downloaded 28 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/cachem_1.0.8.tgz'
Content type 'application/x-gzip' length 67489 bytes (65 KB)
==================================================
downloaded 65 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/Cairo_1.6-0.tgz'
Content type 'application/x-gzip' length 22861382 bytes (21.8 MB)
==================================================
downloaded 21.8 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/class_7.3-22.tgz'
Content type 'application/x-gzip' length 96138 bytes (93 KB)
==================================================
downloaded 93 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/cli_3.6.1.tgz'
Content type 'application/x-gzip' length 1365687 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/cluster_2.1.4.tgz'
Content type 'application/x-gzip' length 616213 bytes (601 KB)
==================================================
downloaded 601 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/curl_5.0.0.tgz'
Content type 'application/x-gzip' length 759005 bytes (741 KB)
==================================================
downloaded 741 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/data.table_1.14.8.tgz'
Content type 'application/x-gzip' length 2376122 bytes (2.3 MB)
==================================================
downloaded 2.3 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/digest_0.6.31.tgz'
Content type 'application/x-gzip' length 298704 bytes (291 KB)
==================================================
downloaded 291 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/dplyr_1.1.2.tgz'
Content type 'application/x-gzip' length 1561346 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/farver_2.1.1.tgz'
Content type 'application/x-gzip' length 1943005 bytes (1.9 MB)
==================================================
downloaded 1.9 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/fastmap_1.1.1.tgz'
Content type 'application/x-gzip' length 201256 bytes (196 KB)
==================================================
downloaded 196 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/foreign_0.8-84.tgz'
Content type 'application/x-gzip' length 331923 bytes (324 KB)
==================================================
downloaded 324 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/fs_1.6.2.tgz'
Content type 'application/x-gzip' length 569071 bytes (555 KB)
==================================================
downloaded 555 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/ggrepel_0.9.3.tgz'
Content type 'application/x-gzip' length 577454 bytes (563 KB)
==================================================
downloaded 563 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/glue_1.6.2.tgz'
Content type 'application/x-gzip' length 151977 bytes (148 KB)
==================================================
downloaded 148 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/htmltools_0.5.5.tgz'
Content type 'application/x-gzip' length 346776 bytes (338 KB)
==================================================
downloaded 338 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/jsonlite_1.8.4.tgz'
Content type 'application/x-gzip' length 1113981 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/KernSmooth_2.23-21.tgz'
Content type 'application/x-gzip' length 100407 bytes (98 KB)
==================================================
downloaded 98 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/later_1.3.1.tgz'
Content type 'application/x-gzip' length 612981 bytes (598 KB)
==================================================
downloaded 598 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/lattice_0.21-8.tgz'
Content type 'application/x-gzip' length 1349836 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/locfit_1.5-9.7.tgz'
Content type 'application/x-gzip' length 772384 bytes (754 KB)
==================================================
downloaded 754 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/maps_3.4.1.tgz'
Content type 'application/x-gzip' length 3105432 bytes (3.0 MB)
==================================================
downloaded 3.0 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/matrixStats_0.63.0.tgz'
Content type 'application/x-gzip' length 592172 bytes (578 KB)
==================================================
downloaded 578 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/mgcv_1.8-42.tgz'
Content type 'application/x-gzip' length 3737078 bytes (3.6 MB)
==================================================
downloaded 3.6 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/mime_0.12.tgz'
Content type 'application/x-gzip' length 34812 bytes (33 KB)
==================================================
downloaded 33 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/nlme_3.1-162.tgz'
Content type 'application/x-gzip' length 2400717 bytes (2.3 MB)
==================================================
downloaded 2.3 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/nnet_7.3-19.tgz'
Content type 'application/x-gzip' length 129034 bytes (126 KB)
==================================================
downloaded 126 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/openssl_2.0.6.tgz'
Content type 'application/x-gzip' length 2886168 bytes (2.8 MB)
==================================================
downloaded 2.8 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/proj4_1.0-12.tgz'
Content type 'application/x-gzip' length 17782645 bytes (17.0 MB)
==================================================
downloaded 17.0 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/promises_1.2.0.1.tgz'
Content type 'application/x-gzip' length 1782018 bytes (1.7 MB)
==================================================
downloaded 1.7 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/purrr_1.0.1.tgz'
Content type 'application/x-gzip' length 509931 bytes (497 KB)
==================================================
downloaded 497 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/ragg_1.2.5.tgz'
Content type 'application/x-gzip' length 9223518 bytes (8.8 MB)
==================================================
downloaded 8.8 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/Rcpp_1.0.10.tgz'
Content type 'application/x-gzip' length 3242867 bytes (3.1 MB)
==================================================
downloaded 3.1 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/RcppArmadillo_0.12.2.0.0.tgz'
Content type 'application/x-gzip' length 1570686 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/RCurl_1.98-1.12.tgz'
Content type 'application/x-gzip' length 1089009 bytes (1.0 MB)
==================================================
downloaded 1.0 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/rlang_1.1.1.tgz'
Content type 'application/x-gzip' length 1852475 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/rpart_4.1.19.tgz'
Content type 'application/x-gzip' length 980040 bytes (957 KB)
==================================================
downloaded 957 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/RSQLite_2.3.1.tgz'
Content type 'application/x-gzip' length 4340278 bytes (4.1 MB)
==================================================
downloaded 4.1 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/sass_0.4.6.tgz'
Content type 'application/x-gzip' length 2392703 bytes (2.3 MB)
==================================================
downloaded 2.3 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/spatial_7.3-16.tgz'
Content type 'application/x-gzip' length 157695 bytes (153 KB)
==================================================
downloaded 153 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/stringi_1.7.12.tgz'
Content type 'application/x-gzip' length 14448461 bytes (13.8 MB)
==================================================
downloaded 13.8 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/survival_3.5-5.tgz'
Content type 'application/x-gzip' length 6768208 bytes (6.5 MB)
==================================================
downloaded 6.5 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/sys_3.4.1.tgz'
Content type 'application/x-gzip' length 47312 bytes (46 KB)
==================================================
downloaded 46 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/systemfonts_1.0.4.tgz'
Content type 'application/x-gzip' length 5900454 bytes (5.6 MB)
==================================================
downloaded 5.6 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/textshaping_0.3.6.tgz'
Content type 'application/x-gzip' length 1291817 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/tibble_3.2.1.tgz'
Content type 'application/x-gzip' length 676416 bytes (660 KB)
==================================================
downloaded 660 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/tidyr_1.3.0.tgz'
Content type 'application/x-gzip' length 1324625 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/tidyselect_1.2.0.tgz'
Content type 'application/x-gzip' length 219384 bytes (214 KB)
==================================================
downloaded 214 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/utf8_1.2.3.tgz'
Content type 'application/x-gzip' length 196912 bytes (192 KB)
==================================================
downloaded 192 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/vctrs_0.6.2.tgz'
Content type 'application/x-gzip' length 1850681 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/xfun_0.39.tgz'
Content type 'application/x-gzip' length 430615 bytes (420 KB)
==================================================
downloaded 420 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/XML_3.99-0.14.tgz'
Content type 'application/x-gzip' length 1873852 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/yaml_2.3.7.tgz'
Content type 'application/x-gzip' length 204951 bytes (200 KB)
==================================================
downloaded 200 KB

The downloaded binary packages are in
    /var/folders/db/_9mqvxh50pb53z2xy8z_xhjr0000gn/T//RtmpapzpFa/downloaded_packages
library(AnnotationDbi)
library(org.Hs.eg.db)
res.df <- as.data.frame(dds.res) # putting the de.sign into a data.frame to help the next step to work
res.annot <- mapIds(org.Hs.eg.db, keys = rownames(res.df), keytype = "ENSEMBL", column = "SYMBOL") #mapping ensembl ids to Gene Symbols
'select()' returned 1:many mapping between keys and columns
res.df.annot <- cbind(res.df,gene.symbol = res.annot) #binding the annotations to the sign.df

head(res.df.annot)

write.csv(res.df.annot, file = "DE_sensitiveVSresistant_results_wGeneSymbol.csv")
EnhancedVolcano(res.df.annot,
    lab = res.df.annot$gene.symbol,
    x = 'log2FoldChange',
    y = 'padj')

Over-representation test

Install R packages and load libraries

BiocManager::install("clusterProfiler")
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")'
for details.
Replacement repositories:
    CRAN: https://cran.rstudio.com/
Bioconductor version 3.15 (BiocManager 1.30.26), R 4.2.3 (2023-03-15)
Installing package(s) 'clusterProfiler'
also installing the dependencies ‘gridGraphics’, ‘tweenr’, ‘polyclip’, ‘RcppArmadillo’, ‘gridExtra’, ‘fastmatch’, ‘ggfun’, ‘ggplotify’, ‘patchwork’, ‘ggforce’, ‘ggrepel’, ‘viridis’, ‘tidygraph’, ‘graphlayouts’, ‘S7’, ‘ape’, ‘tidytree’, ‘treeio’, ‘DO.db’, ‘fgsea’, ‘reshape2’, ‘aplot’, ‘ggraph’, ‘igraph’, ‘scatterpie’, ‘shadowtext’, ‘ggtree’, ‘downloader’, ‘DOSE’, ‘enrichplot’, ‘GOSemSim’, ‘plyr’, ‘qvalue’, ‘yulab.utils’

Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.15/data/annotation/bin/macosx/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.15/data/annotation/bin/macosx/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.15/data/experiment/bin/macosx/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.15/data/experiment/bin/macosx/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.15/workflows/bin/macosx/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.15/workflows/bin/macosx/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 11573Warning: cannot open URL 'https://bioconductor.org/packages/3.15/books/bin/macosx/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 11573Warning: cannot open URL 'https://bioconductor.org/packages/3.15/books/bin/macosx/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'

  There are binary versions available but the source versions are later:
no
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/gridGraphics_0.5-1.tgz'
Content type 'application/x-gzip' length 247355 bytes (241 KB)
==================================================
downloaded 241 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/tweenr_2.0.2.tgz'
Content type 'application/x-gzip' length 783938 bytes (765 KB)
==================================================
downloaded 765 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/polyclip_1.10-6.tgz'
Content type 'application/x-gzip' length 465379 bytes (454 KB)
==================================================
downloaded 454 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/RcppArmadillo_0.12.6.6.1.tgz'
Content type 'application/x-gzip' length 1613879 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/gridExtra_2.3.tgz'
Content type 'application/x-gzip' length 1103175 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/fastmatch_1.1-4.tgz'
Content type 'application/x-gzip' length 50284 bytes (49 KB)
==================================================
downloaded 49 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/ggplotify_0.1.2.tgz'
Content type 'application/x-gzip' length 138434 bytes (135 KB)
==================================================
downloaded 135 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/ggforce_0.4.1.tgz'
Content type 'application/x-gzip' length 4534238 bytes (4.3 MB)
==================================================
downloaded 4.3 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/ggrepel_0.9.4.tgz'
Content type 'application/x-gzip' length 578404 bytes (564 KB)
==================================================
downloaded 564 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/tidygraph_1.3.0.tgz'
Content type 'application/x-gzip' length 632444 bytes (617 KB)
==================================================
downloaded 617 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/graphlayouts_1.0.1.tgz'
Content type 'application/x-gzip' length 4537326 bytes (4.3 MB)
==================================================
downloaded 4.3 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/S7_0.1.1.tgz'
Content type 'application/x-gzip' length 278131 bytes (271 KB)
==================================================
downloaded 271 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/ape_5.7-1.tgz'
Content type 'application/x-gzip' length 3479252 bytes (3.3 MB)
==================================================
downloaded 3.3 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/tidytree_0.4.6.tgz'
Content type 'application/x-gzip' length 336033 bytes (328 KB)
==================================================
downloaded 328 KB

trying URL 'https://bioconductor.org/packages/3.15/bioc/bin/macosx/contrib/4.2/treeio_1.20.2.tgz'
Content type 'application/x-compressed-tar' length 916609 bytes (895 KB)
==================================================
downloaded 895 KB

trying URL 'https://bioconductor.org/packages/3.15/bioc/bin/macosx/contrib/4.2/fgsea_1.22.0.tgz'
Content type 'application/x-compressed-tar' length 1489172 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/reshape2_1.4.4.tgz'
Content type 'application/x-gzip' length 333392 bytes (325 KB)
==================================================
downloaded 325 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/ggraph_2.1.0.tgz'
Content type 'application/x-gzip' length 4652466 bytes (4.4 MB)
==================================================
downloaded 4.4 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/igraph_1.5.1.tgz'
Content type 'application/x-gzip' length 8627201 bytes (8.2 MB)
==================================================
downloaded 8.2 MB

trying URL 'https://bioconductor.org/packages/3.15/bioc/bin/macosx/contrib/4.2/ggtree_3.4.4.tgz'
Content type 'application/x-compressed-tar' length 916106 bytes (894 KB)
==================================================
downloaded 894 KB

trying URL 'https://bioconductor.org/packages/3.15/bioc/bin/macosx/contrib/4.2/DOSE_3.22.1.tgz'
Content type 'application/x-compressed-tar' length 6704314 bytes (6.4 MB)
==================================================
downloaded 6.4 MB

trying URL 'https://bioconductor.org/packages/3.15/bioc/bin/macosx/contrib/4.2/enrichplot_1.16.2.tgz'
Content type 'application/x-compressed-tar' length 283459 bytes (276 KB)
==================================================
downloaded 276 KB

trying URL 'https://bioconductor.org/packages/3.15/bioc/bin/macosx/contrib/4.2/GOSemSim_2.22.0.tgz'
Content type 'application/x-compressed-tar' length 920638 bytes (899 KB)
==================================================
downloaded 899 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/plyr_1.8.9.tgz'
Content type 'application/x-gzip' length 1007143 bytes (983 KB)
==================================================
downloaded 983 KB

trying URL 'https://bioconductor.org/packages/3.15/bioc/bin/macosx/contrib/4.2/qvalue_2.28.0.tgz'
Content type 'application/x-compressed-tar' length 2801783 bytes (2.7 MB)
==================================================
downloaded 2.7 MB

trying URL 'https://bioconductor.org/packages/3.15/bioc/bin/macosx/contrib/4.2/clusterProfiler_4.4.4.tgz'
Content type 'application/x-compressed-tar' length 821345 bytes (802 KB)
==================================================
downloaded 802 KB

The downloaded binary packages are in
    /var/folders/db/_9mqvxh50pb53z2xy8z_xhjr0000gn/T//Rtmp173bOF/downloaded_packages
installing the source packages ‘ggfun’, ‘patchwork’, ‘viridis’, ‘DO.db’, ‘aplot’, ‘scatterpie’, ‘shadowtext’, ‘downloader’, ‘yulab.utils’

trying URL 'https://cran.rstudio.com/src/contrib/ggfun_0.2.0.tar.gz'
Content type 'application/x-gzip' length 110603 bytes (108 KB)
==================================================
downloaded 108 KB

trying URL 'https://cran.rstudio.com/src/contrib/patchwork_1.3.1.tar.gz'
Content type 'application/x-gzip' length 3323546 bytes (3.2 MB)
==================================================
downloaded 3.2 MB

trying URL 'https://cran.rstudio.com/src/contrib/viridis_0.6.5.tar.gz'
Content type 'application/x-gzip' length 3047363 bytes (2.9 MB)
==================================================
downloaded 2.9 MB

trying URL 'https://bioconductor.org/packages/3.15/data/annotation/src/contrib/DO.db_2.9.tar.gz'
Content type 'application/gzip' length 1769978 bytes (1.7 MB)
==================================================
downloaded 1.7 MB

trying URL 'https://cran.rstudio.com/src/contrib/aplot_0.2.8.tar.gz'
Content type 'application/x-gzip' length 56476 bytes (55 KB)
==================================================
downloaded 55 KB

trying URL 'https://cran.rstudio.com/src/contrib/scatterpie_0.2.5.tar.gz'
Content type 'application/x-gzip' length 118875 bytes (116 KB)
==================================================
downloaded 116 KB

trying URL 'https://cran.rstudio.com/src/contrib/shadowtext_0.1.5.tar.gz'
Content type 'application/x-gzip' length 173227 bytes (169 KB)
==================================================
downloaded 169 KB

trying URL 'https://cran.rstudio.com/src/contrib/downloader_0.4.1.tar.gz'
Content type 'application/x-gzip' length 6942 bytes
==================================================
downloaded 6942 bytes

trying URL 'https://cran.rstudio.com/src/contrib/yulab.utils_0.2.0.tar.gz'
Content type 'application/x-gzip' length 25030 bytes (24 KB)
==================================================
downloaded 24 KB

* installing *source* package ‘patchwork’ ...
** package ‘patchwork’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (patchwork)
* installing *source* package ‘viridis’ ...
** package ‘viridis’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (viridis)
* installing *source* package ‘DO.db’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DO.db)
* installing *source* package ‘shadowtext’ ...
** package ‘shadowtext’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (shadowtext)
* installing *source* package ‘downloader’ ...
** package ‘downloader’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (downloader)
* installing *source* package ‘yulab.utils’ ...
** package ‘yulab.utils’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (yulab.utils)
* installing *source* package ‘ggfun’ ...
** package ‘ggfun’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ggfun)
* installing *source* package ‘aplot’ ...
** package ‘aplot’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (aplot)
* installing *source* package ‘scatterpie’ ...
** package ‘scatterpie’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (scatterpie)

The downloaded source packages are in
    ‘/private/var/folders/db/_9mqvxh50pb53z2xy8z_xhjr0000gn/T/Rtmp173bOF/downloaded_packages’
Old packages: 'ape', 'brio', 'curl', 'data.table', 'diffobj', 'fastmatch', 'gert', 'ggforce', 'ggraph', 'ggrepel',
  'graphlayouts', 'httr2', 'igraph', 'KernSmooth', 'mclust', 'nlme', 'openssl', 'polyclip', 'processx', 'profvis', 'ps',
  'purrr', 'ragg', 'RcppArmadillo', 'RCurl', 'restfulr', 'roxygen2', 'rprojroot', 'S7', 'systemfonts', 'testthat',
  'textshaping', 'tidygraph', 'tweenr', 'waldo', 'XML', 'zip'
Update all/some/none? [a/s/n]: 
a
Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.15/data/annotation/bin/macosx/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.15/data/annotation/bin/macosx/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.15/data/experiment/bin/macosx/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.15/data/experiment/bin/macosx/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.15/workflows/bin/macosx/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.15/workflows/bin/macosx/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 11573Warning: cannot open URL 'https://bioconductor.org/packages/3.15/books/bin/macosx/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 11573Warning: cannot open URL 'https://bioconductor.org/packages/3.15/books/bin/macosx/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'

  There are binary versions available but the source versions are later:
no
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/ape_5.7-1.tgz'
Content type 'application/x-gzip' length 3479252 bytes (3.3 MB)
==================================================
downloaded 3.3 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/brio_1.1.4.tgz'
Content type 'application/x-gzip' length 42717 bytes (41 KB)
==================================================
downloaded 41 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/curl_5.2.0.tgz'
Content type 'application/x-gzip' length 791519 bytes (772 KB)
==================================================
downloaded 772 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/data.table_1.14.10.tgz'
Content type 'application/x-gzip' length 2343663 bytes (2.2 MB)
==================================================
downloaded 2.2 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/diffobj_0.3.5.tgz'
Content type 'application/x-gzip' length 1004587 bytes (981 KB)
==================================================
downloaded 981 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/fastmatch_1.1-4.tgz'
Content type 'application/x-gzip' length 50284 bytes (49 KB)
==================================================
downloaded 49 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/gert_2.0.1.tgz'
Content type 'application/x-gzip' length 1998048 bytes (1.9 MB)
==================================================
downloaded 1.9 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/ggforce_0.4.1.tgz'
Content type 'application/x-gzip' length 4534238 bytes (4.3 MB)
==================================================
downloaded 4.3 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/ggraph_2.1.0.tgz'
Content type 'application/x-gzip' length 4652466 bytes (4.4 MB)
==================================================
downloaded 4.4 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/ggrepel_0.9.4.tgz'
Content type 'application/x-gzip' length 578404 bytes (564 KB)
==================================================
downloaded 564 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/graphlayouts_1.0.1.tgz'
Content type 'application/x-gzip' length 4537326 bytes (4.3 MB)
==================================================
downloaded 4.3 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/igraph_1.5.1.tgz'
Content type 'application/x-gzip' length 8627201 bytes (8.2 MB)
==================================================
downloaded 8.2 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/KernSmooth_2.23-22.tgz'
Content type 'application/x-gzip' length 100525 bytes (98 KB)
==================================================
downloaded 98 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/mclust_6.0.1.tgz'
Content type 'application/x-gzip' length 4237708 bytes (4.0 MB)
==================================================
downloaded 4.0 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/nlme_3.1-164.tgz'
Content type 'application/x-gzip' length 2404341 bytes (2.3 MB)
==================================================
downloaded 2.3 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/openssl_2.1.1.tgz'
Content type 'application/x-gzip' length 2886259 bytes (2.8 MB)
==================================================
downloaded 2.8 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/polyclip_1.10-6.tgz'
Content type 'application/x-gzip' length 465379 bytes (454 KB)
==================================================
downloaded 454 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/processx_3.8.3.tgz'
Content type 'application/x-gzip' length 312250 bytes (304 KB)
==================================================
downloaded 304 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/profvis_0.3.8.tgz'
Content type 'application/x-gzip' length 200631 bytes (195 KB)
==================================================
downloaded 195 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/ps_1.7.5.tgz'
Content type 'application/x-gzip' length 308891 bytes (301 KB)
==================================================
downloaded 301 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/purrr_1.0.2.tgz'
Content type 'application/x-gzip' length 510913 bytes (498 KB)
==================================================
downloaded 498 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/ragg_1.2.7.tgz'
Content type 'application/x-gzip' length 9236153 bytes (8.8 MB)
==================================================
downloaded 8.8 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/RcppArmadillo_0.12.6.6.1.tgz'
Content type 'application/x-gzip' length 1613879 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/RCurl_1.98-1.13.tgz'
Content type 'application/x-gzip' length 1092020 bytes (1.0 MB)
==================================================
downloaded 1.0 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/restfulr_0.0.15.tgz'
Content type 'application/x-gzip' length 347166 bytes (339 KB)
==================================================
downloaded 339 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/roxygen2_7.2.3.tgz'
Content type 'application/x-gzip' length 910190 bytes (888 KB)
==================================================
downloaded 888 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/S7_0.1.1.tgz'
Content type 'application/x-gzip' length 278131 bytes (271 KB)
==================================================
downloaded 271 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/systemfonts_1.0.5.tgz'
Content type 'application/x-gzip' length 5898277 bytes (5.6 MB)
==================================================
downloaded 5.6 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/testthat_3.2.1.tgz'
Content type 'application/x-gzip' length 3100512 bytes (3.0 MB)
==================================================
downloaded 3.0 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/textshaping_0.3.7.tgz'
Content type 'application/x-gzip' length 5354762 bytes (5.1 MB)
==================================================
downloaded 5.1 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/tidygraph_1.3.0.tgz'
Content type 'application/x-gzip' length 632444 bytes (617 KB)
==================================================
downloaded 617 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/tweenr_2.0.2.tgz'
Content type 'application/x-gzip' length 783938 bytes (765 KB)
==================================================
downloaded 765 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/XML_3.99-0.16.tgz'
Content type 'application/x-gzip' length 1868841 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/zip_2.3.0.tgz'
Content type 'application/x-gzip' length 211400 bytes (206 KB)
==================================================
downloaded 206 KB

The downloaded binary packages are in
    /var/folders/db/_9mqvxh50pb53z2xy8z_xhjr0000gn/T//Rtmp173bOF/downloaded_packages
installing the source packages ‘httr2’, ‘rprojroot’, ‘waldo’

trying URL 'https://cran.rstudio.com/src/contrib/httr2_1.2.0.tar.gz'
Content type 'application/x-gzip' length 271515 bytes (265 KB)
==================================================
downloaded 265 KB

trying URL 'https://cran.rstudio.com/src/contrib/rprojroot_2.1.0.tar.gz'
Content type 'application/x-gzip' length 59562 bytes (58 KB)
==================================================
downloaded 58 KB

trying URL 'https://cran.rstudio.com/src/contrib/waldo_0.6.2.tar.gz'
Content type 'application/x-gzip' length 45913 bytes (44 KB)
==================================================
downloaded 44 KB

* installing *source* package ‘httr2’ ...
** package ‘httr2’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (httr2)
* installing *source* package ‘rprojroot’ ...
** package ‘rprojroot’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rprojroot)
* installing *source* package ‘waldo’ ...
** package ‘waldo’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (waldo)

The downloaded source packages are in
    ‘/private/var/folders/db/_9mqvxh50pb53z2xy8z_xhjr0000gn/T/Rtmp173bOF/downloaded_packages’
library(clusterProfiler)

Registered S3 method overwritten by 'data.table':
  method           from
  print.data.table     
Registered S3 methods overwritten by 'treeio':
  method              from    
  MRCA.phylo          tidytree
  MRCA.treedata       tidytree
  Nnode.treedata      tidytree
  Ntip.treedata       tidytree
  ancestor.phylo      tidytree
  ancestor.treedata   tidytree
  child.phylo         tidytree
  child.treedata      tidytree
  full_join.phylo     tidytree
  full_join.treedata  tidytree
  groupClade.phylo    tidytree
  groupClade.treedata tidytree
  groupOTU.phylo      tidytree
  groupOTU.treedata   tidytree
  is.rooted.treedata  tidytree
  nodeid.phylo        tidytree
  nodeid.treedata     tidytree
  nodelab.phylo       tidytree
  nodelab.treedata    tidytree
  offspring.phylo     tidytree
  offspring.treedata  tidytree
  parent.phylo        tidytree
  parent.treedata     tidytree
  root.treedata       tidytree
  rootnode.phylo      tidytree
  sibling.phylo       tidytree
clusterProfiler v4.4.4  For help: https://yulab-smu.top/biomedical-knowledge-mining-book/

If you use clusterProfiler in published research, please cite:
T Wu, E Hu, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, W Tang, L Zhan, X Fu, S Liu, X Bo, and G Yu. clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. The Innovation. 2021, 2(3):100141

Attaching package: ‘clusterProfiler’

The following object is masked from ‘package:stats’:

    filter
install.packages("msigdbr")
also installing the dependencies ‘assertthat’, ‘babelgene’

  There is a binary version available but the source version is later:
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/assertthat_0.2.1.tgz'
Content type 'application/x-gzip' length 52693 bytes (51 KB)
==================================================
downloaded 51 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/babelgene_22.9.tgz'
Content type 'application/x-gzip' length 3651754 bytes (3.5 MB)
==================================================
downloaded 3.5 MB

The downloaded binary packages are in
    /var/folders/db/_9mqvxh50pb53z2xy8z_xhjr0000gn/T//Rtmp173bOF/downloaded_packages
installing the source package ‘msigdbr’

trying URL 'https://cran.rstudio.com/src/contrib/msigdbr_25.1.0.tar.gz'
Content type 'application/x-gzip' length 10020 bytes
==================================================
downloaded 10020 bytes

* installing *source* package ‘msigdbr’ ...
** package ‘msigdbr’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (msigdbr)

The downloaded source packages are in
    ‘/private/var/folders/db/_9mqvxh50pb53z2xy8z_xhjr0000gn/T/Rtmp173bOF/downloaded_packages’
library(msigdbr)

msigdbr is an R package that gives you easy access to gene sets from the Molecular Signatures Database (MSigDB) — a widely used resource for gene set enrichment analysis (GSEA).

Load the C5 collection from MSigDB i.e. Gene Ontologies

go_gene_sets <- msigdbr(species = "human", category = "C5")  #Load C5
Warning: The `category` argument of `msigdbr()` is deprecated as of msigdbr 10.0.0.
Please use the `collection` argument instead.
 [0%] Downloaded 1348 bytes...
 [0%] Downloaded 4044 bytes...
 [0%] Downloaded 12236 bytes...
 [0%] Downloaded 13480 bytes...
 [0%] Downloaded 14828 bytes...
 [0%] Downloaded 20272 bytes...
 [0%] Downloaded 36656 bytes...
 [0%] Downloaded 41788 bytes...
 [0%] Downloaded 56668 bytes...
 [0%] Downloaded 62060 bytes...
 [0%] Downloaded 67452 bytes...
 [0%] Downloaded 71496 bytes...
 [0%] Downloaded 74192 bytes...
 [0%] Downloaded 78236 bytes...
 [0%] Downloaded 81468 bytes...
 [0%] Downloaded 85564 bytes...
 [0%] Downloaded 86912 bytes...
 [0%] Downloaded 93756 bytes...
 [0%] Downloaded 95104 bytes...
 [0%] Downloaded 99148 bytes...
 [0%] Downloaded 101844 bytes...
 [0%] Downloaded 108584 bytes...
 [0%] Downloaded 115324 bytes...
 [0%] Downloaded 116216 bytes...
 [0%] Downloaded 118912 bytes...
 [0%] Downloaded 124356 bytes...
 [0%] Downloaded 131200 bytes...
 [0%] Downloaded 132548 bytes...
 [0%] Downloaded 135244 bytes...
 [0%] Downloaded 151628 bytes...
 [0%] Downloaded 154104 bytes...
 [0%] Downloaded 170488 bytes...
 [0%] Downloaded 186808 bytes...
 [0%] Downloaded 203192 bytes...
 [0%] Downloaded 219512 bytes...
 [0%] Downloaded 235896 bytes...
 [0%] Downloaded 252216 bytes...
 [0%] Downloaded 263812 bytes...
 [0%] Downloaded 267856 bytes...
 [0%] Downloaded 284240 bytes...
 [0%] Downloaded 294816 bytes...
 [0%] Downloaded 311200 bytes...
 [0%] Downloaded 316384 bytes...
 [0%] Downloaded 327536 bytes...
 [1%] Downloaded 343920 bytes...
 [1%] Downloaded 343968 bytes...
 [1%] Downloaded 360352 bytes...
 [1%] Downloaded 376056 bytes...
 [1%] Downloaded 379740 bytes...
 [1%] Downloaded 396124 bytes...
 [1%] Downloaded 412444 bytes...
 [1%] Downloaded 428828 bytes...
 [1%] Downloaded 445148 bytes...
 [1%] Downloaded 461532 bytes...
 [1%] Downloaded 477852 bytes...
 [1%] Downloaded 494236 bytes...
 [1%] Downloaded 510556 bytes...
 [1%] Downloaded 510572 bytes...
 [1%] Downloaded 526956 bytes...
 [1%] Downloaded 527004 bytes...
 [1%] Downloaded 543268 bytes...
 [1%] Downloaded 559652 bytes...
 [1%] Downloaded 575972 bytes...
 [1%] Downloaded 592356 bytes...
 [1%] Downloaded 608676 bytes...
 [1%] Downloaded 625060 bytes...
 [1%] Downloaded 641380 bytes...
 [1%] Downloaded 657764 bytes...
 [1%] Downloaded 674084 bytes...
 [2%] Downloaded 690468 bytes...
 [2%] Downloaded 706788 bytes...
 [2%] Downloaded 723172 bytes...
 [2%] Downloaded 739492 bytes...
 [2%] Downloaded 755876 bytes...
 [2%] Downloaded 772196 bytes...
 [2%] Downloaded 788580 bytes...
 [2%] Downloaded 804900 bytes...
 [2%] Downloaded 821284 bytes...
 [2%] Downloaded 837604 bytes...
 [2%] Downloaded 853988 bytes...
 [2%] Downloaded 870308 bytes...
 [2%] Downloaded 886692 bytes...
 [2%] Downloaded 903012 bytes...
 [2%] Downloaded 919396 bytes...
 [2%] Downloaded 935716 bytes...
 [2%] Downloaded 952100 bytes...
 [2%] Downloaded 968420 bytes...
 [2%] Downloaded 984804 bytes...
 [2%] Downloaded 1001124 bytes...
 [3%] Downloaded 1017508 bytes...
 [3%] Downloaded 1033828 bytes...
 [3%] Downloaded 1050212 bytes...
 [3%] Downloaded 1066532 bytes...
 [3%] Downloaded 1082916 bytes...
 [3%] Downloaded 1099236 bytes...
 [3%] Downloaded 1115620 bytes...
 [3%] Downloaded 1131940 bytes...
 [3%] Downloaded 1131956 bytes...
 [3%] Downloaded 1148340 bytes...
 [3%] Downloaded 1148388 bytes...
 [3%] Downloaded 1164652 bytes...
 [3%] Downloaded 1181036 bytes...
 [3%] Downloaded 1197356 bytes...
 [3%] Downloaded 1213740 bytes...
 [3%] Downloaded 1230060 bytes...
 [3%] Downloaded 1246444 bytes...
 [3%] Downloaded 1262764 bytes...
 [3%] Downloaded 1279148 bytes...
 [3%] Downloaded 1295468 bytes...
 [3%] Downloaded 1311852 bytes...
 [3%] Downloaded 1328172 bytes...
 [3%] Downloaded 1344556 bytes...
 [4%] Downloaded 1360876 bytes...
 [4%] Downloaded 1377260 bytes...
 [4%] Downloaded 1393580 bytes...
 [4%] Downloaded 1409964 bytes...
 [4%] Downloaded 1426284 bytes...
 [4%] Downloaded 1442668 bytes...
 [4%] Downloaded 1458988 bytes...
 [4%] Downloaded 1475372 bytes...
 [4%] Downloaded 1491692 bytes...
 [4%] Downloaded 1508076 bytes...
 [4%] Downloaded 1524396 bytes...
 [4%] Downloaded 1540780 bytes...
 [4%] Downloaded 1557100 bytes...
 [4%] Downloaded 1557116 bytes...
 [4%] Downloaded 1573500 bytes...
 [4%] Downloaded 1573548 bytes...
 [4%] Downloaded 1589812 bytes...
 [4%] Downloaded 1606196 bytes...
 [4%] Downloaded 1622516 bytes...
 [4%] Downloaded 1638900 bytes...
 [4%] Downloaded 1655220 bytes...
 [4%] Downloaded 1671604 bytes...
 [5%] Downloaded 1687924 bytes...
 [5%] Downloaded 1704308 bytes...
 [5%] Downloaded 1720628 bytes...
 [5%] Downloaded 1737012 bytes...
 [5%] Downloaded 1753332 bytes...
 [5%] Downloaded 1769716 bytes...
 [5%] Downloaded 1786036 bytes...
 [5%] Downloaded 1802420 bytes...
 [5%] Downloaded 1818740 bytes...
 [5%] Downloaded 1835124 bytes...
 [5%] Downloaded 1851444 bytes...
 [5%] Downloaded 1867828 bytes...
 [5%] Downloaded 1884148 bytes...
 [5%] Downloaded 1900532 bytes...
 [5%] Downloaded 1916852 bytes...
 [5%] Downloaded 1933236 bytes...
 [5%] Downloaded 1949556 bytes...
 [5%] Downloaded 1965940 bytes...
 [5%] Downloaded 1982260 bytes...
 [5%] Downloaded 1998644 bytes...
 [5%] Downloaded 2014964 bytes...
 [6%] Downloaded 2031348 bytes...
 [6%] Downloaded 2047668 bytes...
 [6%] Downloaded 2064052 bytes...
 [6%] Downloaded 2080372 bytes...
 [6%] Downloaded 2096756 bytes...
 [6%] Downloaded 2113076 bytes...
 [6%] Downloaded 2129460 bytes...
 [6%] Downloaded 2145780 bytes...
 [6%] Downloaded 2162164 bytes...
 [6%] Downloaded 2178484 bytes...
 [6%] Downloaded 2194868 bytes...
 [6%] Downloaded 2211188 bytes...
 [6%] Downloaded 2227572 bytes...
 [6%] Downloaded 2243892 bytes...
 [6%] Downloaded 2260276 bytes...
 [6%] Downloaded 2276596 bytes...
 [6%] Downloaded 2292980 bytes...
 [6%] Downloaded 2309300 bytes...
 [6%] Downloaded 2325684 bytes...
 [6%] Downloaded 2342004 bytes...
 [6%] Downloaded 2358388 bytes...
 [7%] Downloaded 2374708 bytes...
 [7%] Downloaded 2391092 bytes...
 [7%] Downloaded 2407412 bytes...
 [7%] Downloaded 2423796 bytes...
 [7%] Downloaded 2440116 bytes...
 [7%] Downloaded 2456500 bytes...
 [7%] Downloaded 2472820 bytes...
 [7%] Downloaded 2489204 bytes...
 [7%] Downloaded 2505524 bytes...
 [7%] Downloaded 2521908 bytes...
 [7%] Downloaded 2538228 bytes...
 [7%] Downloaded 2554612 bytes...
 [7%] Downloaded 2570932 bytes...
 [7%] Downloaded 2587316 bytes...
 [7%] Downloaded 2603636 bytes...
 [7%] Downloaded 2620020 bytes...
 [7%] Downloaded 2636340 bytes...
 [7%] Downloaded 2652724 bytes...
 [7%] Downloaded 2669044 bytes...
 [7%] Downloaded 2685428 bytes...
 [8%] Downloaded 2701748 bytes...
 [8%] Downloaded 2718132 bytes...
 [8%] Downloaded 2734452 bytes...
 [8%] Downloaded 2750836 bytes...
 [8%] Downloaded 2767156 bytes...
 [8%] Downloaded 2783540 bytes...
 [8%] Downloaded 2799860 bytes...
 [8%] Downloaded 2816244 bytes...
 [8%] Downloaded 2832564 bytes...
 [8%] Downloaded 2848948 bytes...
 [8%] Downloaded 2865268 bytes...
 [8%] Downloaded 2881652 bytes...
 [8%] Downloaded 2897972 bytes...
 [8%] Downloaded 2914356 bytes...
 [8%] Downloaded 2930676 bytes...
 [8%] Downloaded 2947060 bytes...
 [8%] Downloaded 2963380 bytes...
 [8%] Downloaded 2979764 bytes...
 [8%] Downloaded 2996084 bytes...
 [8%] Downloaded 3012468 bytes...
 [8%] Downloaded 3028788 bytes...
 [8%] Downloaded 3028804 bytes...
 [9%] Downloaded 3045188 bytes...
 [9%] Downloaded 3045236 bytes...
 [9%] Downloaded 3061500 bytes...
 [9%] Downloaded 3077884 bytes...
 [9%] Downloaded 3094204 bytes...
 [9%] Downloaded 3110588 bytes...
 [9%] Downloaded 3126908 bytes...
 [9%] Downloaded 3143292 bytes...
 [9%] Downloaded 3159612 bytes...
 [9%] Downloaded 3175996 bytes...
 [9%] Downloaded 3192316 bytes...
 [9%] Downloaded 3208700 bytes...
 [9%] Downloaded 3225020 bytes...
 [9%] Downloaded 3241404 bytes...
 [9%] Downloaded 3257724 bytes...
 [9%] Downloaded 3274108 bytes...
 [9%] Downloaded 3290428 bytes...
 [9%] Downloaded 3306812 bytes...
 [9%] Downloaded 3323132 bytes...
 [9%] Downloaded 3339516 bytes...
 [9%] Downloaded 3355836 bytes...
 [9%] Downloaded 3372220 bytes...
 [10%] Downloaded 3388540 bytes...
 [10%] Downloaded 3404924 bytes...
 [10%] Downloaded 3421244 bytes...
 [10%] Downloaded 3437628 bytes...
 [10%] Downloaded 3453948 bytes...
 [10%] Downloaded 3470332 bytes...
 [10%] Downloaded 3486652 bytes...
 [10%] Downloaded 3503036 bytes...
 [10%] Downloaded 3519356 bytes...
 [10%] Downloaded 3535740 bytes...
 [10%] Downloaded 3552060 bytes...
 [10%] Downloaded 3568444 bytes...
 [10%] Downloaded 3584764 bytes...
 [10%] Downloaded 3601148 bytes...
 [10%] Downloaded 3617468 bytes...
 [10%] Downloaded 3633852 bytes...
 [10%] Downloaded 3650172 bytes...
 [10%] Downloaded 3666556 bytes...
 [10%] Downloaded 3682876 bytes...
 [10%] Downloaded 3699260 bytes...
 [11%] Downloaded 3715580 bytes...
 [11%] Downloaded 3731964 bytes...
 [11%] Downloaded 3748284 bytes...
 [11%] Downloaded 3764668 bytes...
 [11%] Downloaded 3780988 bytes...
 [11%] Downloaded 3797372 bytes...
 [11%] Downloaded 3813692 bytes...
 [11%] Downloaded 3830076 bytes...
 [11%] Downloaded 3846396 bytes...
 [11%] Downloaded 3862780 bytes...
 [11%] Downloaded 3879100 bytes...
 [11%] Downloaded 3895484 bytes...
 [11%] Downloaded 3911804 bytes...
 [11%] Downloaded 3928188 bytes...
 [11%] Downloaded 3944508 bytes...
 [11%] Downloaded 3960892 bytes...
 [11%] Downloaded 3977212 bytes...
 [11%] Downloaded 3993596 bytes...
 [11%] Downloaded 4009916 bytes...
 [11%] Downloaded 4026300 bytes...
 [11%] Downloaded 4042620 bytes...
 [12%] Downloaded 4059004 bytes...
 [12%] Downloaded 4075324 bytes...
 [12%] Downloaded 4091708 bytes...
 [12%] Downloaded 4108028 bytes...
 [12%] Downloaded 4124412 bytes...
 [12%] Downloaded 4140732 bytes...
 [12%] Downloaded 4157116 bytes...
 [12%] Downloaded 4173436 bytes...
 [12%] Downloaded 4189820 bytes...
 [12%] Downloaded 4206140 bytes...
 [12%] Downloaded 4222524 bytes...
 [12%] Downloaded 4238844 bytes...
 [12%] Downloaded 4255228 bytes...
 [12%] Downloaded 4271548 bytes...
 [12%] Downloaded 4287932 bytes...
 [12%] Downloaded 4304252 bytes...
 [12%] Downloaded 4320636 bytes...
 [12%] Downloaded 4336956 bytes...
 [12%] Downloaded 4353340 bytes...
 [12%] Downloaded 4369660 bytes...
 [13%] Downloaded 4386044 bytes...
 [13%] Downloaded 4402364 bytes...
 [13%] Downloaded 4418748 bytes...
 [13%] Downloaded 4435068 bytes...
 [13%] Downloaded 4451452 bytes...
 [13%] Downloaded 4467772 bytes...
 [13%] Downloaded 4484156 bytes...
 [13%] Downloaded 4500476 bytes...
 [13%] Downloaded 4516860 bytes...
 [13%] Downloaded 4533180 bytes...
 [13%] Downloaded 4549564 bytes...
 [13%] Downloaded 4565884 bytes...
 [13%] Downloaded 4582268 bytes...
 [13%] Downloaded 4598588 bytes...
 [13%] Downloaded 4614972 bytes...
 [13%] Downloaded 4631292 bytes...
 [13%] Downloaded 4647676 bytes...
 [13%] Downloaded 4663996 bytes...
 [13%] Downloaded 4680380 bytes...
 [13%] Downloaded 4696700 bytes...
 [13%] Downloaded 4713084 bytes...
 [14%] Downloaded 4729404 bytes...
 [14%] Downloaded 4745788 bytes...
 [14%] Downloaded 4762108 bytes...
 [14%] Downloaded 4778492 bytes...
 [14%] Downloaded 4794812 bytes...
 [14%] Downloaded 4811196 bytes...
 [14%] Downloaded 4827516 bytes...
 [14%] Downloaded 4827532 bytes...
 [14%] Downloaded 4843916 bytes...
 [14%] Downloaded 4843964 bytes...
 [14%] Downloaded 4860228 bytes...
 [14%] Downloaded 4876612 bytes...
 [14%] Downloaded 4892932 bytes...
 [14%] Downloaded 4909316 bytes...
 [14%] Downloaded 4925636 bytes...
 [14%] Downloaded 4942020 bytes...
 [14%] Downloaded 4958340 bytes...
 [14%] Downloaded 4974724 bytes...
 [14%] Downloaded 4991044 bytes...
 [14%] Downloaded 4991060 bytes...
 [14%] Downloaded 5007444 bytes...
 [14%] Downloaded 5007492 bytes...
 [14%] Downloaded 5023756 bytes...
 [14%] Downloaded 5040140 bytes...
 [14%] Downloaded 5056460 bytes...
 [15%] Downloaded 5072844 bytes...
 [15%] Downloaded 5089164 bytes...
 [15%] Downloaded 5105548 bytes...
 [15%] Downloaded 5121868 bytes...
 [15%] Downloaded 5138252 bytes...
 [15%] Downloaded 5154572 bytes...
 [15%] Downloaded 5170956 bytes...
 [15%] Downloaded 5187276 bytes...
 [15%] Downloaded 5203660 bytes...
 [15%] Downloaded 5219980 bytes...
 [15%] Downloaded 5219996 bytes...
 [15%] Downloaded 5236380 bytes...
 [15%] Downloaded 5236428 bytes...
 [15%] Downloaded 5252692 bytes...
 [15%] Downloaded 5269076 bytes...
 [15%] Downloaded 5285396 bytes...
 [15%] Downloaded 5301780 bytes...
 [15%] Downloaded 5318100 bytes...
 [15%] Downloaded 5334484 bytes...
 [15%] Downloaded 5350804 bytes...
 [15%] Downloaded 5367188 bytes...
 [15%] Downloaded 5383508 bytes...
 [16%] Downloaded 5399892 bytes...
 [16%] Downloaded 5416212 bytes...
 [16%] Downloaded 5432596 bytes...
 [16%] Downloaded 5448916 bytes...
 [16%] Downloaded 5465300 bytes...
 [16%] Downloaded 5481620 bytes...
 [16%] Downloaded 5498004 bytes...
 [16%] Downloaded 5514324 bytes...
 [16%] Downloaded 5530708 bytes...
 [16%] Downloaded 5547028 bytes...
 [16%] Downloaded 5563412 bytes...
 [16%] Downloaded 5579732 bytes...
 [16%] Downloaded 5596116 bytes...
 [16%] Downloaded 5612436 bytes...
 [16%] Downloaded 5628820 bytes...
 [16%] Downloaded 5645140 bytes...
 [16%] Downloaded 5661524 bytes...
 [16%] Downloaded 5677844 bytes...
 [16%] Downloaded 5694228 bytes...
 [16%] Downloaded 5710548 bytes...
 [16%] Downloaded 5726932 bytes...
 [17%] Downloaded 5743252 bytes...
 [17%] Downloaded 5759636 bytes...
 [17%] Downloaded 5775956 bytes...
 [17%] Downloaded 5792340 bytes...
 [17%] Downloaded 5808660 bytes...
 [17%] Downloaded 5825044 bytes...
 [17%] Downloaded 5841364 bytes...
 [17%] Downloaded 5857748 bytes...
 [17%] Downloaded 5874068 bytes...
 [17%] Downloaded 5874084 bytes...
 [17%] Downloaded 5890468 bytes...
 [17%] Downloaded 5890516 bytes...
 [17%] Downloaded 5906780 bytes...
 [17%] Downloaded 5923164 bytes...
 [17%] Downloaded 5939484 bytes...
 [17%] Downloaded 5955868 bytes...
 [17%] Downloaded 5972188 bytes...
 [17%] Downloaded 5988572 bytes...
 [17%] Downloaded 6004892 bytes...
 [17%] Downloaded 6021276 bytes...
 [17%] Downloaded 6037596 bytes...
 [17%] Downloaded 6037612 bytes...
 [17%] Downloaded 6053996 bytes...
 [17%] Downloaded 6054044 bytes...
 [17%] Downloaded 6070308 bytes...
 [18%] Downloaded 6086692 bytes...
 [18%] Downloaded 6103012 bytes...
 [18%] Downloaded 6119396 bytes...
 [18%] Downloaded 6135716 bytes...
 [18%] Downloaded 6152100 bytes...
 [18%] Downloaded 6168420 bytes...
 [18%] Downloaded 6184804 bytes...
 [18%] Downloaded 6201124 bytes...
 [18%] Downloaded 6217508 bytes...
 [18%] Downloaded 6233828 bytes...
 [18%] Downloaded 6250212 bytes...
 [18%] Downloaded 6266532 bytes...
 [18%] Downloaded 6282916 bytes...
 [18%] Downloaded 6299236 bytes...
 [18%] Downloaded 6315620 bytes...
 [18%] Downloaded 6331940 bytes...
 [18%] Downloaded 6348324 bytes...
 [18%] Downloaded 6364644 bytes...
 [18%] Downloaded 6381028 bytes...
 [18%] Downloaded 6397348 bytes...
 [19%] Downloaded 6413732 bytes...
 [19%] Downloaded 6430052 bytes...
 [19%] Downloaded 6430068 bytes...
 [19%] Downloaded 6446452 bytes...
 [19%] Downloaded 6446500 bytes...
 [19%] Downloaded 6462764 bytes...
 [19%] Downloaded 6479148 bytes...
 [19%] Downloaded 6495468 bytes...
 [19%] Downloaded 6511852 bytes...
 [19%] Downloaded 6528172 bytes...
 [19%] Downloaded 6544556 bytes...
 [19%] Downloaded 6560876 bytes...
 [19%] Downloaded 6577260 bytes...
 [19%] Downloaded 6593580 bytes...
 [19%] Downloaded 6609964 bytes...
 [19%] Downloaded 6626284 bytes...
 [19%] Downloaded 6642668 bytes...
 [19%] Downloaded 6658988 bytes...
 [19%] Downloaded 6675372 bytes...
 [19%] Downloaded 6691692 bytes...
 [19%] Downloaded 6708076 bytes...
 [19%] Downloaded 6724396 bytes...
 [19%] Downloaded 6740780 bytes...
 [20%] Downloaded 6757100 bytes...
 [20%] Downloaded 6773484 bytes...
 [20%] Downloaded 6789804 bytes...
 [20%] Downloaded 6806188 bytes...
 [20%] Downloaded 6822508 bytes...
 [20%] Downloaded 6838892 bytes...
 [20%] Downloaded 6855212 bytes...
 [20%] Downloaded 6871596 bytes...
 [20%] Downloaded 6887916 bytes...
 [20%] Downloaded 6887932 bytes...
 [20%] Downloaded 6904316 bytes...
 [20%] Downloaded 6904364 bytes...
 [20%] Downloaded 6920628 bytes...
 [20%] Downloaded 6937012 bytes...
 [20%] Downloaded 6953332 bytes...
 [20%] Downloaded 6969716 bytes...
 [20%] Downloaded 6986036 bytes...
 [20%] Downloaded 7002420 bytes...
 [20%] Downloaded 7018740 bytes...
 [20%] Downloaded 7035124 bytes...
 [20%] Downloaded 7051444 bytes...
 [20%] Downloaded 7067828 bytes...
 [21%] Downloaded 7084148 bytes...
 [21%] Downloaded 7100532 bytes...
 [21%] Downloaded 7116852 bytes...
 [21%] Downloaded 7133236 bytes...
 [21%] Downloaded 7149556 bytes...
 [21%] Downloaded 7165940 bytes...
 [21%] Downloaded 7182260 bytes...
 [21%] Downloaded 7198644 bytes...
 [21%] Downloaded 7214964 bytes...
 [21%] Downloaded 7231348 bytes...
 [21%] Downloaded 7247668 bytes...
 [21%] Downloaded 7264052 bytes...
 [21%] Downloaded 7280372 bytes...
 [21%] Downloaded 7296756 bytes...
 [21%] Downloaded 7313076 bytes...
 [21%] Downloaded 7329460 bytes...
 [21%] Downloaded 7345780 bytes...
 [21%] Downloaded 7362164 bytes...
 [21%] Downloaded 7378484 bytes...
 [21%] Downloaded 7394868 bytes...
 [21%] Downloaded 7411188 bytes...
 [22%] Downloaded 7427572 bytes...
 [22%] Downloaded 7443892 bytes...
 [22%] Downloaded 7460276 bytes...
 [22%] Downloaded 7476596 bytes...
 [22%] Downloaded 7492980 bytes...
 [22%] Downloaded 7509300 bytes...
 [22%] Downloaded 7525684 bytes...
 [22%] Downloaded 7542004 bytes...
 [22%] Downloaded 7558388 bytes...
 [22%] Downloaded 7574708 bytes...
 [22%] Downloaded 7591092 bytes...
 [22%] Downloaded 7607412 bytes...
 [22%] Downloaded 7623796 bytes...
 [22%] Downloaded 7640116 bytes...
 [22%] Downloaded 7656500 bytes...
 [22%] Downloaded 7672820 bytes...
 [22%] Downloaded 7689204 bytes...
 [22%] Downloaded 7705524 bytes...
 [22%] Downloaded 7721908 bytes...
 [22%] Downloaded 7738228 bytes...
 [22%] Downloaded 7754612 bytes...
 [23%] Downloaded 7770932 bytes...
 [23%] Downloaded 7787316 bytes...
 [23%] Downloaded 7803636 bytes...
 [23%] Downloaded 7820020 bytes...
 [23%] Downloaded 7836340 bytes...
 [23%] Downloaded 7852724 bytes...
 [23%] Downloaded 7869044 bytes...
 [23%] Downloaded 7885428 bytes...
 [23%] Downloaded 7901748 bytes...
 [23%] Downloaded 7901764 bytes...
 [23%] Downloaded 7918148 bytes...
 [23%] Downloaded 7918196 bytes...
 [23%] Downloaded 7934460 bytes...
 [23%] Downloaded 7950844 bytes...
 [23%] Downloaded 7967164 bytes...
 [23%] Downloaded 7983548 bytes...
 [23%] Downloaded 7999868 bytes...
 [23%] Downloaded 8016252 bytes...
 [23%] Downloaded 8032572 bytes...
 [23%] Downloaded 8048956 bytes...
 [23%] Downloaded 8065276 bytes...
 [23%] Downloaded 8081660 bytes...
 [24%] Downloaded 8097980 bytes...
 [24%] Downloaded 8114364 bytes...
 [24%] Downloaded 8130684 bytes...
 [24%] Downloaded 8147068 bytes...
 [24%] Downloaded 8163388 bytes...
 [24%] Downloaded 8179772 bytes...
 [24%] Downloaded 8196092 bytes...
 [24%] Downloaded 8212476 bytes...
 [24%] Downloaded 8228796 bytes...
 [24%] Downloaded 8245180 bytes...
 [24%] Downloaded 8261500 bytes...
 [24%] Downloaded 8277884 bytes...
 [24%] Downloaded 8294204 bytes...
 [24%] Downloaded 8310588 bytes...
 [24%] Downloaded 8326908 bytes...
 [24%] Downloaded 8343292 bytes...
 [24%] Downloaded 8359612 bytes...
 [24%] Downloaded 8359628 bytes...
 [24%] Downloaded 8376012 bytes...
 [24%] Downloaded 8376060 bytes...
 [24%] Downloaded 8392324 bytes...
 [24%] Downloaded 8408708 bytes...
 [24%] Downloaded 8425028 bytes...
 [25%] Downloaded 8441412 bytes...
 [25%] Downloaded 8457732 bytes...
 [25%] Downloaded 8474116 bytes...
 [25%] Downloaded 8490436 bytes...
 [25%] Downloaded 8506820 bytes...
 [25%] Downloaded 8523140 bytes...
 [25%] Downloaded 8539524 bytes...
 [25%] Downloaded 8555844 bytes...
 [25%] Downloaded 8572228 bytes...
 [25%] Downloaded 8588548 bytes...
 [25%] Downloaded 8604932 bytes...
 [25%] Downloaded 8621252 bytes...
 [25%] Downloaded 8637636 bytes...
 [25%] Downloaded 8653956 bytes...
 [25%] Downloaded 8670340 bytes...
 [25%] Downloaded 8686660 bytes...
 [25%] Downloaded 8703044 bytes...
 [25%] Downloaded 8719364 bytes...
 [25%] Downloaded 8735748 bytes...
 [25%] Downloaded 8752068 bytes...
 [25%] Downloaded 8768452 bytes...
 [26%] Downloaded 8784772 bytes...
 [26%] Downloaded 8801156 bytes...
 [26%] Downloaded 8817476 bytes...
 [26%] Downloaded 8833860 bytes...
 [26%] Downloaded 8850180 bytes...
 [26%] Downloaded 8866564 bytes...
 [26%] Downloaded 8882884 bytes...
 [26%] Downloaded 8882900 bytes...
 [26%] Downloaded 8899284 bytes...
 [26%] Downloaded 8899332 bytes...
 [26%] Downloaded 8915596 bytes...
 [26%] Downloaded 8931980 bytes...
 [26%] Downloaded 8948300 bytes...
 [26%] Downloaded 8964684 bytes...
 [26%] Downloaded 8981004 bytes...
 [26%] Downloaded 8997388 bytes...
 [26%] Downloaded 9013708 bytes...
 [26%] Downloaded 9030092 bytes...
 [26%] Downloaded 9046412 bytes...
 [26%] Downloaded 9062796 bytes...
 [26%] Downloaded 9079116 bytes...
 [26%] Downloaded 9095500 bytes...
 [27%] Downloaded 9111820 bytes...
 [27%] Downloaded 9128204 bytes...
 [27%] Downloaded 9144524 bytes...
 [27%] Downloaded 9160908 bytes...
 [27%] Downloaded 9177228 bytes...
 [27%] Downloaded 9193612 bytes...
 [27%] Downloaded 9209932 bytes...
 [27%] Downloaded 9226316 bytes...
 [27%] Downloaded 9242636 bytes...
 [27%] Downloaded 9259020 bytes...
 [27%] Downloaded 9275340 bytes...
 [27%] Downloaded 9291724 bytes...
 [27%] Downloaded 9308044 bytes...
 [27%] Downloaded 9308060 bytes...
 [27%] Downloaded 9324444 bytes...
 [27%] Downloaded 9324492 bytes...
 [27%] Downloaded 9340756 bytes...
 [27%] Downloaded 9357140 bytes...
 [27%] Downloaded 9373460 bytes...
 [27%] Downloaded 9389844 bytes...
 [27%] Downloaded 9406164 bytes...
 [27%] Downloaded 9422548 bytes...
 [27%] Downloaded 9438868 bytes...
 [28%] Downloaded 9455252 bytes...
 [28%] Downloaded 9471572 bytes...
 [28%] Downloaded 9487956 bytes...
 [28%] Downloaded 9504276 bytes...
 [28%] Downloaded 9520660 bytes...
 [28%] Downloaded 9536980 bytes...
 [28%] Downloaded 9553364 bytes...
 [28%] Downloaded 9569684 bytes...
 [28%] Downloaded 9586068 bytes...
 [28%] Downloaded 9602388 bytes...
 [28%] Downloaded 9618772 bytes...
 [28%] Downloaded 9635092 bytes...
 [28%] Downloaded 9651476 bytes...
 [28%] Downloaded 9667796 bytes...
 [28%] Downloaded 9684180 bytes...
 [28%] Downloaded 9700500 bytes...
 [28%] Downloaded 9716884 bytes...
 [28%] Downloaded 9733204 bytes...
 [28%] Downloaded 9749588 bytes...
 [28%] Downloaded 9765908 bytes...
 [29%] Downloaded 9782292 bytes...
 [29%] Downloaded 9798612 bytes...
 [29%] Downloaded 9814996 bytes...
 [29%] Downloaded 9831316 bytes...
 [29%] Downloaded 9847700 bytes...
 [29%] Downloaded 9864020 bytes...
 [29%] Downloaded 9880404 bytes...
 [29%] Downloaded 9896724 bytes...
 [29%] Downloaded 9913108 bytes...
 [29%] Downloaded 9929428 bytes...
 [29%] Downloaded 9945812 bytes...
 [29%] Downloaded 9962132 bytes...
 [29%] Downloaded 9978516 bytes...
 [29%] Downloaded 9994836 bytes...
 [29%] Downloaded 10011220 bytes...
 [29%] Downloaded 10027540 bytes...
 [29%] Downloaded 10043924 bytes...
 [29%] Downloaded 10060244 bytes...
 [29%] Downloaded 10076628 bytes...
 [29%] Downloaded 10092948 bytes...
 [29%] Downloaded 10109332 bytes...
 [30%] Downloaded 10125652 bytes...
 [30%] Downloaded 10142036 bytes...
 [30%] Downloaded 10158356 bytes...
 [30%] Downloaded 10174740 bytes...
 [30%] Downloaded 10191060 bytes...
 [30%] Downloaded 10207444 bytes...
 [30%] Downloaded 10223764 bytes...
 [30%] Downloaded 10240148 bytes...
 [30%] Downloaded 10256468 bytes...
 [30%] Downloaded 10272852 bytes...
 [30%] Downloaded 10289172 bytes...
 [30%] Downloaded 10305556 bytes...
 [30%] Downloaded 10321876 bytes...
 [30%] Downloaded 10338260 bytes...
 [30%] Downloaded 10354580 bytes...
 [30%] Downloaded 10370964 bytes...
 [30%] Downloaded 10387284 bytes...
 [30%] Downloaded 10403668 bytes...
 [30%] Downloaded 10419988 bytes...
 [30%] Downloaded 10436372 bytes...
 [30%] Downloaded 10452692 bytes...
 [31%] Downloaded 10469076 bytes...
 [31%] Downloaded 10485396 bytes...
 [31%] Downloaded 10501780 bytes...
 [31%] Downloaded 10518100 bytes...
 [31%] Downloaded 10534484 bytes...
 [31%] Downloaded 10550804 bytes...
 [31%] Downloaded 10567188 bytes...
 [31%] Downloaded 10583508 bytes...
 [31%] Downloaded 10599892 bytes...
 [31%] Downloaded 10616212 bytes...
 [31%] Downloaded 10632596 bytes...
 [31%] Downloaded 10648916 bytes...
 [31%] Downloaded 10665300 bytes...
 [31%] Downloaded 10681620 bytes...
 [31%] Downloaded 10698004 bytes...
 [31%] Downloaded 10714324 bytes...
 [31%] Downloaded 10730708 bytes...
 [31%] Downloaded 10747028 bytes...
 [31%] Downloaded 10763412 bytes...
 [31%] Downloaded 10779732 bytes...
 [32%] Downloaded 10796116 bytes...
 [32%] Downloaded 10812436 bytes...
 [32%] Downloaded 10828820 bytes...
 [32%] Downloaded 10845140 bytes...
 [32%] Downloaded 10861524 bytes...
 [32%] Downloaded 10877844 bytes...
 [32%] Downloaded 10894228 bytes...
 [32%] Downloaded 10910548 bytes...
 [32%] Downloaded 10926932 bytes...
 [32%] Downloaded 10943252 bytes...
 [32%] Downloaded 10959636 bytes...
 [32%] Downloaded 10975956 bytes...
 [32%] Downloaded 10992340 bytes...
 [32%] Downloaded 11008660 bytes...
 [32%] Downloaded 11025044 bytes...
 [32%] Downloaded 11041364 bytes...
 [32%] Downloaded 11057748 bytes...
 [32%] Downloaded 11074068 bytes...
 [32%] Downloaded 11090452 bytes...
 [32%] Downloaded 11106772 bytes...
 [32%] Downloaded 11123156 bytes...
 [33%] Downloaded 11139476 bytes...
 [33%] Downloaded 11155860 bytes...
 [33%] Downloaded 11172180 bytes...
 [33%] Downloaded 11188564 bytes...
 [33%] Downloaded 11204884 bytes...
 [33%] Downloaded 11221268 bytes...
 [33%] Downloaded 11237588 bytes...
 [33%] Downloaded 11253972 bytes...
 [33%] Downloaded 11270292 bytes...
 [33%] Downloaded 11286676 bytes...
 [33%] Downloaded 11302996 bytes...
 [33%] Downloaded 11319380 bytes...
 [33%] Downloaded 11335700 bytes...
 [33%] Downloaded 11352084 bytes...
 [33%] Downloaded 11368404 bytes...
 [33%] Downloaded 11384788 bytes...
 [33%] Downloaded 11401108 bytes...
 [33%] Downloaded 11417492 bytes...
 [33%] Downloaded 11433812 bytes...
 [33%] Downloaded 11450196 bytes...
 [33%] Downloaded 11466516 bytes...
 [34%] Downloaded 11482900 bytes...
 [34%] Downloaded 11499220 bytes...
 [34%] Downloaded 11515604 bytes...
 [34%] Downloaded 11531924 bytes...
 [34%] Downloaded 11548308 bytes...
 [34%] Downloaded 11564628 bytes...
 [34%] Downloaded 11581012 bytes...
 [34%] Downloaded 11597332 bytes...
 [34%] Downloaded 11613716 bytes...
 [34%] Downloaded 11630036 bytes...
 [34%] Downloaded 11646420 bytes...
 [34%] Downloaded 11662740 bytes...
 [34%] Downloaded 11679124 bytes...
 [34%] Downloaded 11695444 bytes...
 [34%] Downloaded 11711828 bytes...
 [34%] Downloaded 11728148 bytes...
 [34%] Downloaded 11744532 bytes...
 [34%] Downloaded 11760852 bytes...
 [34%] Downloaded 11777236 bytes...
 [34%] Downloaded 11793556 bytes...
 [35%] Downloaded 11809940 bytes...
 [35%] Downloaded 11826260 bytes...
 [35%] Downloaded 11842644 bytes...
 [35%] Downloaded 11858964 bytes...
 [35%] Downloaded 11875348 bytes...
 [35%] Downloaded 11891668 bytes...
 [35%] Downloaded 11908052 bytes...
 [35%] Downloaded 11924372 bytes...
 [35%] Downloaded 11940756 bytes...
 [35%] Downloaded 11957076 bytes...
 [35%] Downloaded 11973460 bytes...
 [35%] Downloaded 11989780 bytes...
 [35%] Downloaded 12006164 bytes...
 [35%] Downloaded 12022484 bytes...
 [35%] Downloaded 12038868 bytes...
 [35%] Downloaded 12055188 bytes...
 [35%] Downloaded 12071572 bytes...
 [35%] Downloaded 12087892 bytes...
 [35%] Downloaded 12104276 bytes...
 [35%] Downloaded 12120596 bytes...
 [35%] Downloaded 12136980 bytes...
 [36%] Downloaded 12153300 bytes...
 [36%] Downloaded 12169684 bytes...
 [36%] Downloaded 12186004 bytes...
 [36%] Downloaded 12202388 bytes...
 [36%] Downloaded 12218708 bytes...
 [36%] Downloaded 12235092 bytes...
 [36%] Downloaded 12251412 bytes...
 [36%] Downloaded 12267796 bytes...
 [36%] Downloaded 12284116 bytes...
 [36%] Downloaded 12300500 bytes...
 [36%] Downloaded 12316820 bytes...
 [36%] Downloaded 12333204 bytes...
 [36%] Downloaded 12349524 bytes...
 [36%] Downloaded 12365908 bytes...
 [36%] Downloaded 12382228 bytes...
 [36%] Downloaded 12398612 bytes...
 [36%] Downloaded 12414932 bytes...
 [36%] Downloaded 12431316 bytes...
 [36%] Downloaded 12447636 bytes...
 [36%] Downloaded 12464020 bytes...
 [37%] Downloaded 12480340 bytes...
 [37%] Downloaded 12480356 bytes...
 [37%] Downloaded 12496740 bytes...
 [37%] Downloaded 12496788 bytes...
 [37%] Downloaded 12513052 bytes...
 [37%] Downloaded 12529436 bytes...
 [37%] Downloaded 12545756 bytes...
 [37%] Downloaded 12562140 bytes...
 [37%] Downloaded 12578460 bytes...
 [37%] Downloaded 12594844 bytes...
 [37%] Downloaded 12611164 bytes...
 [37%] Downloaded 12627548 bytes...
 [37%] Downloaded 12643868 bytes...
 [37%] Downloaded 12660252 bytes...
 [37%] Downloaded 12676572 bytes...
 [37%] Downloaded 12676588 bytes...
 [37%] Downloaded 12692972 bytes...
 [37%] Downloaded 12693020 bytes...
 [37%] Downloaded 12709284 bytes...
 [37%] Downloaded 12725668 bytes...
 [37%] Downloaded 12741988 bytes...
 [37%] Downloaded 12758372 bytes...
 [37%] Downloaded 12774692 bytes...
 [37%] Downloaded 12791076 bytes...
 [37%] Downloaded 12807396 bytes...
 [38%] Downloaded 12823780 bytes...
 [38%] Downloaded 12840100 bytes...
 [38%] Downloaded 12856484 bytes...
 [38%] Downloaded 12872804 bytes...
 [38%] Downloaded 12872820 bytes...
 [38%] Downloaded 12889204 bytes...
 [38%] Downloaded 12889252 bytes...
 [38%] Downloaded 12905516 bytes...
 [38%] Downloaded 12921900 bytes...
 [38%] Downloaded 12938220 bytes...
 [38%] Downloaded 12954604 bytes...
 [38%] Downloaded 12970924 bytes...
 [38%] Downloaded 12987308 bytes...
 [38%] Downloaded 13003628 bytes...
 [38%] Downloaded 13020012 bytes...
 [38%] Downloaded 13036332 bytes...
 [38%] Downloaded 13052716 bytes...
 [38%] Downloaded 13069036 bytes...
 [38%] Downloaded 13069052 bytes...
 [38%] Downloaded 13085436 bytes...
 [38%] Downloaded 13085484 bytes...
 [38%] Downloaded 13101748 bytes...
 [38%] Downloaded 13118132 bytes...
 [38%] Downloaded 13134452 bytes...
 [38%] Downloaded 13150836 bytes...
 [39%] Downloaded 13167156 bytes...
 [39%] Downloaded 13183540 bytes...
 [39%] Downloaded 13199860 bytes...
 [39%] Downloaded 13216244 bytes...
 [39%] Downloaded 13232564 bytes...
 [39%] Downloaded 13248948 bytes...
 [39%] Downloaded 13265268 bytes...
 [39%] Downloaded 13281652 bytes...
 [39%] Downloaded 13297972 bytes...
 [39%] Downloaded 13314356 bytes...
 [39%] Downloaded 13330676 bytes...
 [39%] Downloaded 13330692 bytes...
 [39%] Downloaded 13347076 bytes...
 [39%] Downloaded 13347124 bytes...
 [39%] Downloaded 13363388 bytes...
 [39%] Downloaded 13379772 bytes...
 [39%] Downloaded 13396092 bytes...
 [39%] Downloaded 13412476 bytes...
 [39%] Downloaded 13428796 bytes...
 [39%] Downloaded 13445180 bytes...
 [39%] Downloaded 13461500 bytes...
 [39%] Downloaded 13477884 bytes...
 [40%] Downloaded 13494204 bytes...
 [40%] Downloaded 13510588 bytes...
 [40%] Downloaded 13526908 bytes...
 [40%] Downloaded 13543292 bytes...
 [40%] Downloaded 13559612 bytes...
 [40%] Downloaded 13559628 bytes...
 [40%] Downloaded 13576012 bytes...
 [40%] Downloaded 13576060 bytes...
 [40%] Downloaded 13592324 bytes...
 [40%] Downloaded 13608708 bytes...
 [40%] Downloaded 13625028 bytes...
 [40%] Downloaded 13641412 bytes...
 [40%] Downloaded 13657732 bytes...
 [40%] Downloaded 13674116 bytes...
 [40%] Downloaded 13690436 bytes...
 [40%] Downloaded 13706820 bytes...
 [40%] Downloaded 13723140 bytes...
 [40%] Downloaded 13739524 bytes...
 [40%] Downloaded 13755844 bytes...
 [40%] Downloaded 13772228 bytes...
 [40%] Downloaded 13788548 bytes...
 [40%] Downloaded 13788564 bytes...
 [40%] Downloaded 13804948 bytes...
 [40%] Downloaded 13804996 bytes...
 [40%] Downloaded 13821260 bytes...
 [41%] Downloaded 13837644 bytes...
 [41%] Downloaded 13853964 bytes...
 [41%] Downloaded 13870348 bytes...
 [41%] Downloaded 13886668 bytes...
 [41%] Downloaded 13903052 bytes...
 [41%] Downloaded 13919372 bytes...
 [41%] Downloaded 13935756 bytes...
 [41%] Downloaded 13952076 bytes...
 [41%] Downloaded 13968460 bytes...
 [41%] Downloaded 13984780 bytes...
 [41%] Downloaded 14001164 bytes...
 [41%] Downloaded 14017484 bytes...
 [41%] Downloaded 14017500 bytes...
 [41%] Downloaded 14033884 bytes...
 [41%] Downloaded 14033932 bytes...
 [41%] Downloaded 14050196 bytes...
 [41%] Downloaded 14066580 bytes...
 [41%] Downloaded 14082900 bytes...
 [41%] Downloaded 14099284 bytes...
 [41%] Downloaded 14115604 bytes...
 [41%] Downloaded 14131988 bytes...
 [41%] Downloaded 14148308 bytes...
 [41%] Downloaded 14164692 bytes...
 [42%] Downloaded 14181012 bytes...
 [42%] Downloaded 14197396 bytes...
 [42%] Downloaded 14213716 bytes...
 [42%] Downloaded 14230100 bytes...
 [42%] Downloaded 14246420 bytes...
 [42%] Downloaded 14246436 bytes...
 [42%] Downloaded 14262820 bytes...
 [42%] Downloaded 14262868 bytes...
 [42%] Downloaded 14279132 bytes...
 [42%] Downloaded 14295516 bytes...
 [42%] Downloaded 14311836 bytes...
 [42%] Downloaded 14328220 bytes...
 [42%] Downloaded 14344540 bytes...
 [42%] Downloaded 14360924 bytes...
 [42%] Downloaded 14377244 bytes...
 [42%] Downloaded 14393628 bytes...
 [42%] Downloaded 14409948 bytes...
 [42%] Downloaded 14426332 bytes...
 [42%] Downloaded 14442652 bytes...
 [42%] Downloaded 14459036 bytes...
 [42%] Downloaded 14475356 bytes...
 [42%] Downloaded 14475372 bytes...
 [42%] Downloaded 14491756 bytes...
 [42%] Downloaded 14491804 bytes...
 [43%] Downloaded 14508068 bytes...
 [43%] Downloaded 14524452 bytes...
 [43%] Downloaded 14540772 bytes...
 [43%] Downloaded 14557156 bytes...
 [43%] Downloaded 14573476 bytes...
 [43%] Downloaded 14589860 bytes...
 [43%] Downloaded 14606180 bytes...
 [43%] Downloaded 14622564 bytes...
 [43%] Downloaded 14638884 bytes...
 [43%] Downloaded 14655268 bytes...
 [43%] Downloaded 14671588 bytes...
 [43%] Downloaded 14687972 bytes...
 [43%] Downloaded 14704292 bytes...
 [43%] Downloaded 14704308 bytes...
 [43%] Downloaded 14720692 bytes...
 [43%] Downloaded 14720740 bytes...
 [43%] Downloaded 14737004 bytes...
 [43%] Downloaded 14753388 bytes...
 [43%] Downloaded 14769708 bytes...
 [43%] Downloaded 14786092 bytes...
 [43%] Downloaded 14802412 bytes...
 [43%] Downloaded 14818796 bytes...
 [43%] Downloaded 14835116 bytes...
 [44%] Downloaded 14851500 bytes...
 [44%] Downloaded 14867820 bytes...
 [44%] Downloaded 14884204 bytes...
 [44%] Downloaded 14900524 bytes...
 [44%] Downloaded 14916908 bytes...
 [44%] Downloaded 14933228 bytes...
 [44%] Downloaded 14949612 bytes...
 [44%] Downloaded 14965932 bytes...
 [44%] Downloaded 14982316 bytes...
 [44%] Downloaded 14998636 bytes...
 [44%] Downloaded 15015020 bytes...
 [44%] Downloaded 15031340 bytes...
 [44%] Downloaded 15047724 bytes...
 [44%] Downloaded 15064044 bytes...
 [44%] Downloaded 15080428 bytes...
 [44%] Downloaded 15096748 bytes...
 [44%] Downloaded 15113132 bytes...
 [44%] Downloaded 15129452 bytes...
 [44%] Downloaded 15145836 bytes...
 [44%] Downloaded 15162156 bytes...
 [44%] Downloaded 15178540 bytes...
 [45%] Downloaded 15194860 bytes...
 [45%] Downloaded 15211244 bytes...
 [45%] Downloaded 15227564 bytes...
 [45%] Downloaded 15243948 bytes...
 [45%] Downloaded 15260268 bytes...
 [45%] Downloaded 15276652 bytes...
 [45%] Downloaded 15292972 bytes...
 [45%] Downloaded 15309356 bytes...
 [45%] Downloaded 15325676 bytes...
 [45%] Downloaded 15342060 bytes...
 [45%] Downloaded 15358380 bytes...
 [45%] Downloaded 15374764 bytes...
 [45%] Downloaded 15391084 bytes...
 [45%] Downloaded 15407468 bytes...
 [45%] Downloaded 15423788 bytes...
 [45%] Downloaded 15440172 bytes...
 [45%] Downloaded 15456492 bytes...
 [45%] Downloaded 15472876 bytes...
 [45%] Downloaded 15489196 bytes...
 [45%] Downloaded 15505580 bytes...
 [46%] Downloaded 15521900 bytes...
 [46%] Downloaded 15538284 bytes...
 [46%] Downloaded 15554604 bytes...
 [46%] Downloaded 15570988 bytes...
 [46%] Downloaded 15587308 bytes...
 [46%] Downloaded 15603692 bytes...
 [46%] Downloaded 15620012 bytes...
 [46%] Downloaded 15636396 bytes...
 [46%] Downloaded 15652716 bytes...
 [46%] Downloaded 15669100 bytes...
 [46%] Downloaded 15685420 bytes...
 [46%] Downloaded 15701804 bytes...
 [46%] Downloaded 15718124 bytes...
 [46%] Downloaded 15734508 bytes...
 [46%] Downloaded 15750828 bytes...
 [46%] Downloaded 15767212 bytes...
 [46%] Downloaded 15783532 bytes...
 [46%] Downloaded 15799916 bytes...
 [46%] Downloaded 15816236 bytes...
 [46%] Downloaded 15832620 bytes...
 [46%] Downloaded 15848940 bytes...
 [46%] Downloaded 15848956 bytes...
 [47%] Downloaded 15865340 bytes...
 [47%] Downloaded 15865388 bytes...
 [47%] Downloaded 15881652 bytes...
 [47%] Downloaded 15898036 bytes...
 [47%] Downloaded 15914356 bytes...
 [47%] Downloaded 15930740 bytes...
 [47%] Downloaded 15947060 bytes...
 [47%] Downloaded 15963444 bytes...
 [47%] Downloaded 15979764 bytes...
 [47%] Downloaded 15996148 bytes...
 [47%] Downloaded 16012468 bytes...
 [47%] Downloaded 16028852 bytes...
 [47%] Downloaded 16045172 bytes...
 [47%] Downloaded 16045188 bytes...
 [47%] Downloaded 16061572 bytes...
 [47%] Downloaded 16061620 bytes...
 [47%] Downloaded 16077884 bytes...
 [47%] Downloaded 16094268 bytes...
 [47%] Downloaded 16110588 bytes...
 [47%] Downloaded 16126972 bytes...
 [47%] Downloaded 16143292 bytes...
 [47%] Downloaded 16159676 bytes...
 [47%] Downloaded 16175996 bytes...
 [48%] Downloaded 16192380 bytes...
 [48%] Downloaded 16208700 bytes...
 [48%] Downloaded 16225084 bytes...
 [48%] Downloaded 16241404 bytes...
 [48%] Downloaded 16257788 bytes...
 [48%] Downloaded 16274108 bytes...
 [48%] Downloaded 16290492 bytes...
 [48%] Downloaded 16306812 bytes...
 [48%] Downloaded 16323196 bytes...
 [48%] Downloaded 16339516 bytes...
 [48%] Downloaded 16355900 bytes...
 [48%] Downloaded 16372220 bytes...
 [48%] Downloaded 16388604 bytes...
 [48%] Downloaded 16404924 bytes...
 [48%] Downloaded 16421308 bytes...
 [48%] Downloaded 16437628 bytes...
 [48%] Downloaded 16454012 bytes...
 [48%] Downloaded 16470332 bytes...
 [48%] Downloaded 16486716 bytes...
 [48%] Downloaded 16503036 bytes...
 [48%] Downloaded 16519420 bytes...
 [49%] Downloaded 16535740 bytes...
 [49%] Downloaded 16552124 bytes...
 [49%] Downloaded 16568444 bytes...
 [49%] Downloaded 16584828 bytes...
 [49%] Downloaded 16601148 bytes...
 [49%] Downloaded 16617532 bytes...
 [49%] Downloaded 16633852 bytes...
 [49%] Downloaded 16650236 bytes...
 [49%] Downloaded 16666556 bytes...
 [49%] Downloaded 16682940 bytes...
 [49%] Downloaded 16699260 bytes...
 [49%] Downloaded 16715644 bytes...
 [49%] Downloaded 16731964 bytes...
 [49%] Downloaded 16748348 bytes...
 [49%] Downloaded 16764668 bytes...
 [49%] Downloaded 16781052 bytes...
 [49%] Downloaded 16797372 bytes...
 [49%] Downloaded 16813756 bytes...
 [49%] Downloaded 16830076 bytes...
 [49%] Downloaded 16846460 bytes...
 [49%] Downloaded 16862780 bytes...
 [50%] Downloaded 16879164 bytes...
 [50%] Downloaded 16895484 bytes...
 [50%] Downloaded 16911868 bytes...
 [50%] Downloaded 16928188 bytes...
 [50%] Downloaded 16944572 bytes...
 [50%] Downloaded 16960892 bytes...
 [50%] Downloaded 16977276 bytes...
 [50%] Downloaded 16993596 bytes...
 [50%] Downloaded 17009980 bytes...
 [50%] Downloaded 17026300 bytes...
 [50%] Downloaded 17042684 bytes...
 [50%] Downloaded 17059004 bytes...
 [50%] Downloaded 17075388 bytes...
 [50%] Downloaded 17091708 bytes...
 [50%] Downloaded 17108092 bytes...
 [50%] Downloaded 17124412 bytes...
 [50%] Downloaded 17140796 bytes...
 [50%] Downloaded 17157116 bytes...
 [50%] Downloaded 17173500 bytes...
 [50%] Downloaded 17189820 bytes...
 [51%] Downloaded 17206204 bytes...
 [51%] Downloaded 17222524 bytes...
 [51%] Downloaded 17238908 bytes...
 [51%] Downloaded 17255228 bytes...
 [51%] Downloaded 17271612 bytes...
 [51%] Downloaded 17287932 bytes...
 [51%] Downloaded 17304316 bytes...
 [51%] Downloaded 17320636 bytes...
 [51%] Downloaded 17337020 bytes...
 [51%] Downloaded 17353340 bytes...
 [51%] Downloaded 17369724 bytes...
 [51%] Downloaded 17386044 bytes...
 [51%] Downloaded 17402428 bytes...
 [51%] Downloaded 17418748 bytes...
 [51%] Downloaded 17435132 bytes...
 [51%] Downloaded 17451452 bytes...
 [51%] Downloaded 17467836 bytes...
 [51%] Downloaded 17484156 bytes...
 [51%] Downloaded 17500540 bytes...
 [51%] Downloaded 17516860 bytes...
 [51%] Downloaded 17533244 bytes...
 [52%] Downloaded 17549564 bytes...
 [52%] Downloaded 17565948 bytes...
 [52%] Downloaded 17582268 bytes...
 [52%] Downloaded 17598652 bytes...
 [52%] Downloaded 17614972 bytes...
 [52%] Downloaded 17631356 bytes...
 [52%] Downloaded 17647676 bytes...
 [52%] Downloaded 17664060 bytes...
 [52%] Downloaded 17680380 bytes...
 [52%] Downloaded 17696764 bytes...
 [52%] Downloaded 17713084 bytes...
 [52%] Downloaded 17729468 bytes...
 [52%] Downloaded 17745788 bytes...
 [52%] Downloaded 17762172 bytes...
 [52%] Downloaded 17778492 bytes...
 [52%] Downloaded 17794876 bytes...
 [52%] Downloaded 17811196 bytes...
 [52%] Downloaded 17827580 bytes...
 [52%] Downloaded 17843900 bytes...
 [52%] Downloaded 17860284 bytes...
 [52%] Downloaded 17876604 bytes...
 [53%] Downloaded 17892988 bytes...
 [53%] Downloaded 17909308 bytes...
 [53%] Downloaded 17925692 bytes...
 [53%] Downloaded 17942012 bytes...
 [53%] Downloaded 17958396 bytes...
 [53%] Downloaded 17974716 bytes...
 [53%] Downloaded 17991100 bytes...
 [53%] Downloaded 18007420 bytes...
 [53%] Downloaded 18023804 bytes...
 [53%] Downloaded 18040124 bytes...
 [53%] Downloaded 18056508 bytes...
 [53%] Downloaded 18072828 bytes...
 [53%] Downloaded 18089212 bytes...
 [53%] Downloaded 18105532 bytes...
 [53%] Downloaded 18121916 bytes...
 [53%] Downloaded 18138236 bytes...
 [53%] Downloaded 18154620 bytes...
 [53%] Downloaded 18170940 bytes...
 [53%] Downloaded 18187324 bytes...
 [53%] Downloaded 18203644 bytes...
 [54%] Downloaded 18220028 bytes...
 [54%] Downloaded 18236348 bytes...
 [54%] Downloaded 18252732 bytes...
 [54%] Downloaded 18269052 bytes...
 [54%] Downloaded 18285436 bytes...
 [54%] Downloaded 18301756 bytes...
 [54%] Downloaded 18318140 bytes...
 [54%] Downloaded 18334460 bytes...
 [54%] Downloaded 18350844 bytes...
 [54%] Downloaded 18367164 bytes...
 [54%] Downloaded 18383548 bytes...
 [54%] Downloaded 18399868 bytes...
 [54%] Downloaded 18416252 bytes...
 [54%] Downloaded 18432572 bytes...
 [54%] Downloaded 18448956 bytes...
 [54%] Downloaded 18465276 bytes...
 [54%] Downloaded 18481660 bytes...
 [54%] Downloaded 18497980 bytes...
 [54%] Downloaded 18514364 bytes...
 [54%] Downloaded 18530684 bytes...
 [54%] Downloaded 18547068 bytes...
 [55%] Downloaded 18563388 bytes...
 [55%] Downloaded 18579772 bytes...
 [55%] Downloaded 18596092 bytes...
 [55%] Downloaded 18612476 bytes...
 [55%] Downloaded 18628796 bytes...
 [55%] Downloaded 18645180 bytes...
 [55%] Downloaded 18661500 bytes...
 [55%] Downloaded 18677884 bytes...
 [55%] Downloaded 18694204 bytes...
 [55%] Downloaded 18710588 bytes...
 [55%] Downloaded 18726908 bytes...
 [55%] Downloaded 18743292 bytes...
 [55%] Downloaded 18759612 bytes...
 [55%] Downloaded 18775996 bytes...
 [55%] Downloaded 18792316 bytes...
 [55%] Downloaded 18808700 bytes...
 [55%] Downloaded 18825020 bytes...
 [55%] Downloaded 18841404 bytes...
 [55%] Downloaded 18857724 bytes...
 [55%] Downloaded 18874108 bytes...
 [56%] Downloaded 18890428 bytes...
 [56%] Downloaded 18906812 bytes...
 [56%] Downloaded 18923132 bytes...
 [56%] Downloaded 18939516 bytes...
 [56%] Downloaded 18955836 bytes...
 [56%] Downloaded 18955852 bytes...
 [56%] Downloaded 18972236 bytes...
 [56%] Downloaded 18972284 bytes...
 [56%] Downloaded 18988548 bytes...
 [56%] Downloaded 19004932 bytes...
 [56%] Downloaded 19021252 bytes...
 [56%] Downloaded 19037636 bytes...
 [56%] Downloaded 19053956 bytes...
 [56%] Downloaded 19070340 bytes...
 [56%] Downloaded 19086660 bytes...
 [56%] Downloaded 19103044 bytes...
 [56%] Downloaded 19119364 bytes...
 [56%] Downloaded 19135748 bytes...
 [56%] Downloaded 19152068 bytes...
 [56%] Downloaded 19168452 bytes...
 [56%] Downloaded 19184772 bytes...
 [56%] Downloaded 19201156 bytes...
 [56%] Downloaded 19217476 bytes...
 [56%] Downloaded 19217492 bytes...
 [57%] Downloaded 19233876 bytes...
 [57%] Downloaded 19233924 bytes...
 [57%] Downloaded 19250188 bytes...
 [57%] Downloaded 19266572 bytes...
 [57%] Downloaded 19282892 bytes...
 [57%] Downloaded 19299276 bytes...
 [57%] Downloaded 19315596 bytes...
 [57%] Downloaded 19331980 bytes...
 [57%] Downloaded 19348300 bytes...
 [57%] Downloaded 19364684 bytes...
 [57%] Downloaded 19381004 bytes...
 [57%] Downloaded 19397388 bytes...
 [57%] Downloaded 19413708 bytes...
 [57%] Downloaded 19430092 bytes...
 [57%] Downloaded 19446412 bytes...
 [57%] Downloaded 19446428 bytes...
 [57%] Downloaded 19462812 bytes...
 [57%] Downloaded 19462860 bytes...
 [57%] Downloaded 19479124 bytes...
 [57%] Downloaded 19495508 bytes...
 [57%] Downloaded 19511828 bytes...
 [57%] Downloaded 19528212 bytes...
 [57%] Downloaded 19544532 bytes...
 [57%] Downloaded 19560916 bytes...
 [58%] Downloaded 19577236 bytes...
 [58%] Downloaded 19593620 bytes...
 [58%] Downloaded 19609940 bytes...
 [58%] Downloaded 19626324 bytes...
 [58%] Downloaded 19642644 bytes...
 [58%] Downloaded 19659028 bytes...
 [58%] Downloaded 19675348 bytes...
 [58%] Downloaded 19675364 bytes...
 [58%] Downloaded 19691748 bytes...
 [58%] Downloaded 19691796 bytes...
 [58%] Downloaded 19708060 bytes...
 [58%] Downloaded 19724444 bytes...
 [58%] Downloaded 19740764 bytes...
 [58%] Downloaded 19757148 bytes...
 [58%] Downloaded 19773468 bytes...
 [58%] Downloaded 19789852 bytes...
 [58%] Downloaded 19806172 bytes...
 [58%] Downloaded 19822556 bytes...
 [58%] Downloaded 19838876 bytes...
 [58%] Downloaded 19855260 bytes...
 [58%] Downloaded 19871580 bytes...
 [58%] Downloaded 19887964 bytes...
 [59%] Downloaded 19904284 bytes...
 [59%] Downloaded 19904300 bytes...
 [59%] Downloaded 19920684 bytes...
 [59%] Downloaded 19920732 bytes...
 [59%] Downloaded 19936996 bytes...
 [59%] Downloaded 19953380 bytes...
 [59%] Downloaded 19969700 bytes...
 [59%] Downloaded 19986084 bytes...
 [59%] Downloaded 20002404 bytes...
 [59%] Downloaded 20018788 bytes...
 [59%] Downloaded 20035108 bytes...
 [59%] Downloaded 20051492 bytes...
 [59%] Downloaded 20067812 bytes...
 [59%] Downloaded 20084196 bytes...
 [59%] Downloaded 20100516 bytes...
 [59%] Downloaded 20116900 bytes...
 [59%] Downloaded 20133220 bytes...
 [59%] Downloaded 20149604 bytes...
 [59%] Downloaded 20165924 bytes...
 [59%] Downloaded 20182308 bytes...
 [59%] Downloaded 20198628 bytes...
 [59%] Downloaded 20215012 bytes...
 [59%] Downloaded 20231332 bytes...
 [60%] Downloaded 20247716 bytes...
 [60%] Downloaded 20264036 bytes...
 [60%] Downloaded 20280420 bytes...
 [60%] Downloaded 20296740 bytes...
 [60%] Downloaded 20313124 bytes...
 [60%] Downloaded 20329444 bytes...
 [60%] Downloaded 20345828 bytes...
 [60%] Downloaded 20362148 bytes...
 [60%] Downloaded 20378532 bytes...
 [60%] Downloaded 20394852 bytes...
 [60%] Downloaded 20411236 bytes...
 [60%] Downloaded 20427556 bytes...
 [60%] Downloaded 20443940 bytes...
 [60%] Downloaded 20460260 bytes...
 [60%] Downloaded 20476644 bytes...
 [60%] Downloaded 20492964 bytes...
 [60%] Downloaded 20492980 bytes...
 [60%] Downloaded 20509364 bytes...
 [60%] Downloaded 20509412 bytes...
 [60%] Downloaded 20525676 bytes...
 [60%] Downloaded 20542060 bytes...
 [60%] Downloaded 20558380 bytes...
 [60%] Downloaded 20574764 bytes...
 [61%] Downloaded 20591084 bytes...
 [61%] Downloaded 20607468 bytes...
 [61%] Downloaded 20623788 bytes...
 [61%] Downloaded 20640172 bytes...
 [61%] Downloaded 20656492 bytes...
 [61%] Downloaded 20656508 bytes...
 [61%] Downloaded 20672892 bytes...
 [61%] Downloaded 20672940 bytes...
 [61%] Downloaded 20689204 bytes...
 [61%] Downloaded 20705588 bytes...
 [61%] Downloaded 20721908 bytes...
 [61%] Downloaded 20738292 bytes...
 [61%] Downloaded 20754612 bytes...
 [61%] Downloaded 20770996 bytes...
 [61%] Downloaded 20787316 bytes...
 [61%] Downloaded 20803700 bytes...
 [61%] Downloaded 20820020 bytes...
 [61%] Downloaded 20820036 bytes...
 [61%] Downloaded 20836420 bytes...
 [61%] Downloaded 20836468 bytes...
 [61%] Downloaded 20852732 bytes...
 [61%] Downloaded 20869116 bytes...
 [61%] Downloaded 20885436 bytes...
 [61%] Downloaded 20901820 bytes...
 [62%] Downloaded 20918140 bytes...
 [62%] Downloaded 20934524 bytes...
 [62%] Downloaded 20950844 bytes...
 [62%] Downloaded 20967228 bytes...
 [62%] Downloaded 20983548 bytes...
 [62%] Downloaded 20999932 bytes...
 [62%] Downloaded 21016252 bytes...
 [62%] Downloaded 21032636 bytes...
 [62%] Downloaded 21048956 bytes...
 [62%] Downloaded 21048972 bytes...
 [62%] Downloaded 21065356 bytes...
 [62%] Downloaded 21065404 bytes...
 [62%] Downloaded 21081668 bytes...
 [62%] Downloaded 21098052 bytes...
 [62%] Downloaded 21114372 bytes...
 [62%] Downloaded 21130756 bytes...
 [62%] Downloaded 21147076 bytes...
 [62%] Downloaded 21163460 bytes...
 [62%] Downloaded 21179780 bytes...
 [62%] Downloaded 21196164 bytes...
 [62%] Downloaded 21212484 bytes...
 [62%] Downloaded 21228868 bytes...
 [62%] Downloaded 21245188 bytes...
 [63%] Downloaded 21261572 bytes...
 [63%] Downloaded 21277892 bytes...
 [63%] Downloaded 21294276 bytes...
 [63%] Downloaded 21310596 bytes...
 [63%] Downloaded 21326980 bytes...
 [63%] Downloaded 21343300 bytes...
 [63%] Downloaded 21359684 bytes...
 [63%] Downloaded 21376004 bytes...
 [63%] Downloaded 21392388 bytes...
 [63%] Downloaded 21408708 bytes...
 [63%] Downloaded 21425092 bytes...
 [63%] Downloaded 21441412 bytes...
 [63%] Downloaded 21457796 bytes...
 [63%] Downloaded 21474116 bytes...
 [63%] Downloaded 21474132 bytes...
 [63%] Downloaded 21490516 bytes...
 [63%] Downloaded 21490564 bytes...
 [63%] Downloaded 21506828 bytes...
 [63%] Downloaded 21523212 bytes...
 [63%] Downloaded 21539532 bytes...
 [63%] Downloaded 21555916 bytes...
 [63%] Downloaded 21572236 bytes...
 [64%] Downloaded 21588620 bytes...
 [64%] Downloaded 21604940 bytes...
 [64%] Downloaded 21621324 bytes...
 [64%] Downloaded 21637644 bytes...
 [64%] Downloaded 21654028 bytes...
 [64%] Downloaded 21670348 bytes...
 [64%] Downloaded 21670364 bytes...
 [64%] Downloaded 21686748 bytes...
 [64%] Downloaded 21686796 bytes...
 [64%] Downloaded 21703060 bytes...
 [64%] Downloaded 21719444 bytes...
 [64%] Downloaded 21735764 bytes...
 [64%] Downloaded 21752148 bytes...
 [64%] Downloaded 21768468 bytes...
 [64%] Downloaded 21784852 bytes...
 [64%] Downloaded 21801172 bytes...
 [64%] Downloaded 21817556 bytes...
 [64%] Downloaded 21833876 bytes...
 [64%] Downloaded 21850260 bytes...
 [64%] Downloaded 21866580 bytes...
 [64%] Downloaded 21882964 bytes...
 [64%] Downloaded 21899284 bytes...
 [64%] Downloaded 21899300 bytes...
 [64%] Downloaded 21915684 bytes...
 [64%] Downloaded 21915732 bytes...
 [65%] Downloaded 21931996 bytes...
 [65%] Downloaded 21948380 bytes...
 [65%] Downloaded 21964700 bytes...
 [65%] Downloaded 21981084 bytes...
 [65%] Downloaded 21997404 bytes...
 [65%] Downloaded 22013788 bytes...
 [65%] Downloaded 22030108 bytes...
 [65%] Downloaded 22046492 bytes...
 [65%] Downloaded 22062812 bytes...
 [65%] Downloaded 22079196 bytes...
 [65%] Downloaded 22095516 bytes...
 [65%] Downloaded 22111900 bytes...
 [65%] Downloaded 22128220 bytes...
 [65%] Downloaded 22128236 bytes...
 [65%] Downloaded 22144620 bytes...
 [65%] Downloaded 22144668 bytes...
 [65%] Downloaded 22160932 bytes...
 [65%] Downloaded 22177316 bytes...
 [65%] Downloaded 22193636 bytes...
 [65%] Downloaded 22210020 bytes...
 [65%] Downloaded 22226340 bytes...
 [65%] Downloaded 22242724 bytes...
 [65%] Downloaded 22259044 bytes...
 [66%] Downloaded 22275428 bytes...
 [66%] Downloaded 22291748 bytes...
 [66%] Downloaded 22308132 bytes...
 [66%] Downloaded 22324452 bytes...
 [66%] Downloaded 22340836 bytes...
 [66%] Downloaded 22357156 bytes...
 [66%] Downloaded 22373540 bytes...
 [66%] Downloaded 22389860 bytes...
 [66%] Downloaded 22406244 bytes...
 [66%] Downloaded 22422564 bytes...
 [66%] Downloaded 22438948 bytes...
 [66%] Downloaded 22455268 bytes...
 [66%] Downloaded 22471652 bytes...
 [66%] Downloaded 22487972 bytes...
 [66%] Downloaded 22504356 bytes...
 [66%] Downloaded 22520676 bytes...
 [66%] Downloaded 22537060 bytes...
 [66%] Downloaded 22553380 bytes...
 [66%] Downloaded 22569764 bytes...
 [66%] Downloaded 22586084 bytes...
 [67%] Downloaded 22602468 bytes...
 [67%] Downloaded 22618788 bytes...
 [67%] Downloaded 22635172 bytes...
 [67%] Downloaded 22651492 bytes...
 [67%] Downloaded 22667876 bytes...
 [67%] Downloaded 22684196 bytes...
 [67%] Downloaded 22700580 bytes...
 [67%] Downloaded 22716900 bytes...
 [67%] Downloaded 22716916 bytes...
 [67%] Downloaded 22733300 bytes...
 [67%] Downloaded 22733348 bytes...
 [67%] Downloaded 22749612 bytes...
 [67%] Downloaded 22765996 bytes...
 [67%] Downloaded 22782316 bytes...
 [67%] Downloaded 22798700 bytes...
 [67%] Downloaded 22815020 bytes...
 [67%] Downloaded 22831404 bytes...
 [67%] Downloaded 22847724 bytes...
 [67%] Downloaded 22864108 bytes...
 [67%] Downloaded 22880428 bytes...
 [67%] Downloaded 22896812 bytes...
 [67%] Downloaded 22913132 bytes...
 [67%] Downloaded 22929516 bytes...
 [68%] Downloaded 22945836 bytes...
 [68%] Downloaded 22962220 bytes...
 [68%] Downloaded 22978540 bytes...
 [68%] Downloaded 22994924 bytes...
 [68%] Downloaded 23011244 bytes...
 [68%] Downloaded 23011260 bytes...
 [68%] Downloaded 23027644 bytes...
 [68%] Downloaded 23027692 bytes...
 [68%] Downloaded 23043956 bytes...
 [68%] Downloaded 23060340 bytes...
 [68%] Downloaded 23076660 bytes...
 [68%] Downloaded 23093044 bytes...
 [68%] Downloaded 23109364 bytes...
 [68%] Downloaded 23125748 bytes...
 [68%] Downloaded 23142068 bytes...
 [68%] Downloaded 23158452 bytes...
 [68%] Downloaded 23174772 bytes...
 [68%] Downloaded 23191156 bytes...
 [68%] Downloaded 23207476 bytes...
 [68%] Downloaded 23223860 bytes...
 [68%] Downloaded 23240180 bytes...
 [68%] Downloaded 23240196 bytes...
 [68%] Downloaded 23256580 bytes...
 [68%] Downloaded 23256628 bytes...
 [68%] Downloaded 23272892 bytes...
 [69%] Downloaded 23289276 bytes...
 [69%] Downloaded 23305596 bytes...
 [69%] Downloaded 23321980 bytes...
 [69%] Downloaded 23338300 bytes...
 [69%] Downloaded 23354684 bytes...
 [69%] Downloaded 23371004 bytes...
 [69%] Downloaded 23387388 bytes...
 [69%] Downloaded 23403708 bytes...
 [69%] Downloaded 23420092 bytes...
 [69%] Downloaded 23436412 bytes...
 [69%] Downloaded 23436428 bytes...
 [69%] Downloaded 23452812 bytes...
 [69%] Downloaded 23452860 bytes...
 [69%] Downloaded 23469124 bytes...
 [69%] Downloaded 23485508 bytes...
 [69%] Downloaded 23501828 bytes...
 [69%] Downloaded 23518212 bytes...
 [69%] Downloaded 23534532 bytes...
 [69%] Downloaded 23550916 bytes...
 [69%] Downloaded 23567236 bytes...
 [69%] Downloaded 23583620 bytes...
 [69%] Downloaded 23599940 bytes...
 [70%] Downloaded 23616324 bytes...
 [70%] Downloaded 23632644 bytes...
 [70%] Downloaded 23649028 bytes...
 [70%] Downloaded 23665348 bytes...
 [70%] Downloaded 23665364 bytes...
 [70%] Downloaded 23681748 bytes...
 [70%] Downloaded 23681796 bytes...
 [70%] Downloaded 23698060 bytes...
 [70%] Downloaded 23714444 bytes...
 [70%] Downloaded 23730764 bytes...
 [70%] Downloaded 23747148 bytes...
 [70%] Downloaded 23763468 bytes...
 [70%] Downloaded 23779852 bytes...
 [70%] Downloaded 23796172 bytes...
 [70%] Downloaded 23812556 bytes...
 [70%] Downloaded 23828876 bytes...
 [70%] Downloaded 23845260 bytes...
 [70%] Downloaded 23861580 bytes...
 [70%] Downloaded 23861596 bytes...
 [70%] Downloaded 23877980 bytes...
 [70%] Downloaded 23878028 bytes...
 [70%] Downloaded 23894292 bytes...
 [70%] Downloaded 23910676 bytes...
 [70%] Downloaded 23926996 bytes...
 [70%] Downloaded 23943380 bytes...
 [71%] Downloaded 23959700 bytes...
 [71%] Downloaded 23976084 bytes...
 [71%] Downloaded 23992404 bytes...
 [71%] Downloaded 24008788 bytes...
 [71%] Downloaded 24025108 bytes...
 [71%] Downloaded 24041492 bytes...
 [71%] Downloaded 24057812 bytes...
 [71%] Downloaded 24074196 bytes...
 [71%] Downloaded 24090516 bytes...
 [71%] Downloaded 24090532 bytes...
 [71%] Downloaded 24106916 bytes...
 [71%] Downloaded 24106964 bytes...
 [71%] Downloaded 24123228 bytes...
 [71%] Downloaded 24139612 bytes...
 [71%] Downloaded 24155932 bytes...
 [71%] Downloaded 24172316 bytes...
 [71%] Downloaded 24188636 bytes...
 [71%] Downloaded 24205020 bytes...
 [71%] Downloaded 24221340 bytes...
 [71%] Downloaded 24237724 bytes...
 [71%] Downloaded 24254044 bytes...
 [71%] Downloaded 24270428 bytes...
 [72%] Downloaded 24286748 bytes...
 [72%] Downloaded 24303132 bytes...
 [72%] Downloaded 24319452 bytes...
 [72%] Downloaded 24319468 bytes...
 [72%] Downloaded 24335852 bytes...
 [72%] Downloaded 24335900 bytes...
 [72%] Downloaded 24352164 bytes...
 [72%] Downloaded 24368548 bytes...
 [72%] Downloaded 24384868 bytes...
 [72%] Downloaded 24401252 bytes...
 [72%] Downloaded 24417572 bytes...
 [72%] Downloaded 24433956 bytes...
 [72%] Downloaded 24450276 bytes...
 [72%] Downloaded 24466660 bytes...
 [72%] Downloaded 24482980 bytes...
 [72%] Downloaded 24499364 bytes...
 [72%] Downloaded 24515684 bytes...
 [72%] Downloaded 24515700 bytes...
 [72%] Downloaded 24532084 bytes...
 [72%] Downloaded 24532132 bytes...
 [72%] Downloaded 24548396 bytes...
 [72%] Downloaded 24564780 bytes...
 [72%] Downloaded 24581100 bytes...
 [72%] Downloaded 24597484 bytes...
 [72%] Downloaded 24613804 bytes...
 [73%] Downloaded 24630188 bytes...
 [73%] Downloaded 24646508 bytes...
 [73%] Downloaded 24662892 bytes...
 [73%] Downloaded 24679212 bytes...
 [73%] Downloaded 24695596 bytes...
 [73%] Downloaded 24711916 bytes...
 [73%] Downloaded 24728300 bytes...
 [73%] Downloaded 24744620 bytes...
 [73%] Downloaded 24761004 bytes...
 [73%] Downloaded 24777324 bytes...
 [73%] Downloaded 24793708 bytes...
 [73%] Downloaded 24810028 bytes...
 [73%] Downloaded 24826412 bytes...
 [73%] Downloaded 24842732 bytes...
 [73%] Downloaded 24859116 bytes...
 [73%] Downloaded 24875436 bytes...
 [73%] Downloaded 24891820 bytes...
 [73%] Downloaded 24908140 bytes...
 [73%] Downloaded 24924524 bytes...
 [73%] Downloaded 24940844 bytes...
 [73%] Downloaded 24957228 bytes...
 [74%] Downloaded 24973548 bytes...
 [74%] Downloaded 24973564 bytes...
 [74%] Downloaded 24989948 bytes...
 [74%] Downloaded 24989996 bytes...
 [74%] Downloaded 25006260 bytes...
 [74%] Downloaded 25022644 bytes...
 [74%] Downloaded 25038964 bytes...
 [74%] Downloaded 25055348 bytes...
 [74%] Downloaded 25071668 bytes...
 [74%] Downloaded 25088052 bytes...
 [74%] Downloaded 25104372 bytes...
 [74%] Downloaded 25120756 bytes...
 [74%] Downloaded 25137076 bytes...
 [74%] Downloaded 25153460 bytes...
 [74%] Downloaded 25169780 bytes...
 [74%] Downloaded 25186164 bytes...
 [74%] Downloaded 25202484 bytes...
 [74%] Downloaded 25202500 bytes...
 [74%] Downloaded 25218884 bytes...
 [74%] Downloaded 25218932 bytes...
 [74%] Downloaded 25235196 bytes...
 [74%] Downloaded 25251580 bytes...
 [74%] Downloaded 25267900 bytes...
 [74%] Downloaded 25284284 bytes...
 [75%] Downloaded 25300604 bytes...
 [75%] Downloaded 25316988 bytes...
 [75%] Downloaded 25333308 bytes...
 [75%] Downloaded 25349692 bytes...
 [75%] Downloaded 25366012 bytes...
 [75%] Downloaded 25382396 bytes...
 [75%] Downloaded 25398716 bytes...
 [75%] Downloaded 25415100 bytes...
 [75%] Downloaded 25431420 bytes...
 [75%] Downloaded 25447804 bytes...
 [75%] Downloaded 25464124 bytes...
 [75%] Downloaded 25480508 bytes...
 [75%] Downloaded 25496828 bytes...
 [75%] Downloaded 25513212 bytes...
 [75%] Downloaded 25529532 bytes...
 [75%] Downloaded 25545916 bytes...
 [75%] Downloaded 25562236 bytes...
 [75%] Downloaded 25578620 bytes...
 [75%] Downloaded 25594940 bytes...
 [75%] Downloaded 25594956 bytes...
 [75%] Downloaded 25611340 bytes...
 [75%] Downloaded 25611388 bytes...
 [75%] Downloaded 25627652 bytes...
 [76%] Downloaded 25644036 bytes...
 [76%] Downloaded 25660356 bytes...
 [76%] Downloaded 25676740 bytes...
 [76%] Downloaded 25693060 bytes...
 [76%] Downloaded 25709444 bytes...
 [76%] Downloaded 25725764 bytes...
 [76%] Downloaded 25742148 bytes...
 [76%] Downloaded 25758468 bytes...
 [76%] Downloaded 25758484 bytes...
 [76%] Downloaded 25774868 bytes...
 [76%] Downloaded 25774916 bytes...
 [76%] Downloaded 25791180 bytes...
 [76%] Downloaded 25807564 bytes...
 [76%] Downloaded 25823884 bytes...
 [76%] Downloaded 25840268 bytes...
 [76%] Downloaded 25856588 bytes...
 [76%] Downloaded 25872972 bytes...
 [76%] Downloaded 25889292 bytes...
 [76%] Downloaded 25905676 bytes...
 [76%] Downloaded 25921996 bytes...
 [76%] Downloaded 25922012 bytes...
 [76%] Downloaded 25938396 bytes...
 [76%] Downloaded 25938444 bytes...
 [76%] Downloaded 25954708 bytes...
 [76%] Downloaded 25971092 bytes...
 [77%] Downloaded 25987412 bytes...
 [77%] Downloaded 26003796 bytes...
 [77%] Downloaded 26020116 bytes...
 [77%] Downloaded 26036500 bytes...
 [77%] Downloaded 26052820 bytes...
 [77%] Downloaded 26069204 bytes...
 [77%] Downloaded 26085524 bytes...
 [77%] Downloaded 26101908 bytes...
 [77%] Downloaded 26118228 bytes...
 [77%] Downloaded 26134612 bytes...
 [77%] Downloaded 26150932 bytes...
 [77%] Downloaded 26150948 bytes...
 [77%] Downloaded 26167332 bytes...
 [77%] Downloaded 26167380 bytes...
 [77%] Downloaded 26183644 bytes...
 [77%] Downloaded 26200028 bytes...
 [77%] Downloaded 26216348 bytes...
 [77%] Downloaded 26232732 bytes...
 [77%] Downloaded 26249052 bytes...
 [77%] Downloaded 26265436 bytes...
 [77%] Downloaded 26281756 bytes...
 [77%] Downloaded 26298140 bytes...
 [78%] Downloaded 26314460 bytes...
 [78%] Downloaded 26330844 bytes...
 [78%] Downloaded 26347164 bytes...
 [78%] Downloaded 26363548 bytes...
 [78%] Downloaded 26379868 bytes...
 [78%] Downloaded 26396252 bytes...
 [78%] Downloaded 26412572 bytes...
 [78%] Downloaded 26428956 bytes...
 [78%] Downloaded 26445276 bytes...
 [78%] Downloaded 26445292 bytes...
 [78%] Downloaded 26461676 bytes...
 [78%] Downloaded 26461724 bytes...
 [78%] Downloaded 26477988 bytes...
 [78%] Downloaded 26494372 bytes...
 [78%] Downloaded 26510692 bytes...
 [78%] Downloaded 26527076 bytes...
 [78%] Downloaded 26543396 bytes...
 [78%] Downloaded 26559780 bytes...
 [78%] Downloaded 26576100 bytes...
 [78%] Downloaded 26592484 bytes...
 [78%] Downloaded 26608804 bytes...
 [78%] Downloaded 26625188 bytes...
 [78%] Downloaded 26641508 bytes...
 [79%] Downloaded 26657892 bytes...
 [79%] Downloaded 26674212 bytes...
 [79%] Downloaded 26674228 bytes...
 [79%] Downloaded 26690612 bytes...
 [79%] Downloaded 26690660 bytes...
 [79%] Downloaded 26706924 bytes...
 [79%] Downloaded 26723308 bytes...
 [79%] Downloaded 26739628 bytes...
 [79%] Downloaded 26756012 bytes...
 [79%] Downloaded 26772332 bytes...
 [79%] Downloaded 26788716 bytes...
 [79%] Downloaded 26805036 bytes...
 [79%] Downloaded 26821420 bytes...
 [79%] Downloaded 26837740 bytes...
 [79%] Downloaded 26854124 bytes...
 [79%] Downloaded 26870444 bytes...
 [79%] Downloaded 26870460 bytes...
 [79%] Downloaded 26886844 bytes...
 [79%] Downloaded 26886892 bytes...
 [79%] Downloaded 26903156 bytes...
 [79%] Downloaded 26919540 bytes...
 [79%] Downloaded 26935860 bytes...
 [79%] Downloaded 26952244 bytes...
 [79%] Downloaded 26968564 bytes...
 [80%] Downloaded 26984948 bytes...
 [80%] Downloaded 27001268 bytes...
 [80%] Downloaded 27017652 bytes...
 [80%] Downloaded 27033972 bytes...
 [80%] Downloaded 27050356 bytes...
 [80%] Downloaded 27066676 bytes...
 [80%] Downloaded 27083060 bytes...
 [80%] Downloaded 27099380 bytes...
 [80%] Downloaded 27115764 bytes...
 [80%] Downloaded 27132084 bytes...
 [80%] Downloaded 27148468 bytes...
 [80%] Downloaded 27164788 bytes...
 [80%] Downloaded 27181172 bytes...
 [80%] Downloaded 27197492 bytes...
 [80%] Downloaded 27213876 bytes...
 [80%] Downloaded 27230196 bytes...
 [80%] Downloaded 27246580 bytes...
 [80%] Downloaded 27262900 bytes...
 [80%] Downloaded 27279284 bytes...
 [80%] Downloaded 27295604 bytes...
 [80%] Downloaded 27311988 bytes...
 [81%] Downloaded 27328308 bytes...
 [81%] Downloaded 27344692 bytes...
 [81%] Downloaded 27361012 bytes...
 [81%] Downloaded 27361028 bytes...
 [81%] Downloaded 27377412 bytes...
 [81%] Downloaded 27377460 bytes...
 [81%] Downloaded 27393724 bytes...
 [81%] Downloaded 27410108 bytes...
 [81%] Downloaded 27426428 bytes...
 [81%] Downloaded 27442812 bytes...
 [81%] Downloaded 27459132 bytes...
 [81%] Downloaded 27475516 bytes...
 [81%] Downloaded 27491836 bytes...
 [81%] Downloaded 27508220 bytes...
 [81%] Downloaded 27524540 bytes...
 [81%] Downloaded 27540924 bytes...
 [81%] Downloaded 27557244 bytes...
 [81%] Downloaded 27573628 bytes...
 [81%] Downloaded 27589948 bytes...
 [81%] Downloaded 27606332 bytes...
 [81%] Downloaded 27622652 bytes...
 [81%] Downloaded 27639036 bytes...
 [81%] Downloaded 27655356 bytes...
 [82%] Downloaded 27671740 bytes...
 [82%] Downloaded 27688060 bytes...
 [82%] Downloaded 27704444 bytes...
 [82%] Downloaded 27720764 bytes...
 [82%] Downloaded 27737148 bytes...
 [82%] Downloaded 27753468 bytes...
 [82%] Downloaded 27769852 bytes...
 [82%] Downloaded 27786172 bytes...
 [82%] Downloaded 27802556 bytes...
 [82%] Downloaded 27818876 bytes...
 [82%] Downloaded 27835260 bytes...
 [82%] Downloaded 27851580 bytes...
 [82%] Downloaded 27867964 bytes...
 [82%] Downloaded 27884284 bytes...
 [82%] Downloaded 27900668 bytes...
 [82%] Downloaded 27916988 bytes...
 [82%] Downloaded 27933372 bytes...
 [82%] Downloaded 27949692 bytes...
 [82%] Downloaded 27966076 bytes...
 [82%] Downloaded 27982396 bytes...
 [83%] Downloaded 27998780 bytes...
 [83%] Downloaded 28015100 bytes...
 [83%] Downloaded 28031484 bytes...
 [83%] Downloaded 28047804 bytes...
 [83%] Downloaded 28064188 bytes...
 [83%] Downloaded 28080508 bytes...
 [83%] Downloaded 28096892 bytes...
 [83%] Downloaded 28113212 bytes...
 [83%] Downloaded 28129596 bytes...
 [83%] Downloaded 28145916 bytes...
 [83%] Downloaded 28162300 bytes...
 [83%] Downloaded 28178620 bytes...
 [83%] Downloaded 28195004 bytes...
 [83%] Downloaded 28211324 bytes...
 [83%] Downloaded 28227708 bytes...
 [83%] Downloaded 28244028 bytes...
 [83%] Downloaded 28260412 bytes...
 [83%] Downloaded 28276732 bytes...
 [83%] Downloaded 28293116 bytes...
 [83%] Downloaded 28309436 bytes...
 [83%] Downloaded 28325820 bytes...
 [84%] Downloaded 28342140 bytes...
 [84%] Downloaded 28358524 bytes...
 [84%] Downloaded 28374844 bytes...
 [84%] Downloaded 28391228 bytes...
 [84%] Downloaded 28407548 bytes...
 [84%] Downloaded 28423932 bytes...
 [84%] Downloaded 28440252 bytes...
 [84%] Downloaded 28456636 bytes...
 [84%] Downloaded 28472956 bytes...
 [84%] Downloaded 28489340 bytes...
 [84%] Downloaded 28505660 bytes...
 [84%] Downloaded 28522044 bytes...
 [84%] Downloaded 28538364 bytes...
 [84%] Downloaded 28554748 bytes...
 [84%] Downloaded 28571068 bytes...
 [84%] Downloaded 28587452 bytes...
 [84%] Downloaded 28603772 bytes...
 [84%] Downloaded 28603788 bytes...
 [84%] Downloaded 28620172 bytes...
 [84%] Downloaded 28620220 bytes...
 [84%] Downloaded 28636484 bytes...
 [84%] Downloaded 28652868 bytes...
 [84%] Downloaded 28669188 bytes...
 [85%] Downloaded 28685572 bytes...
 [85%] Downloaded 28701892 bytes...
 [85%] Downloaded 28718276 bytes...
 [85%] Downloaded 28734596 bytes...
 [85%] Downloaded 28750980 bytes...
 [85%] Downloaded 28767300 bytes...
 [85%] Downloaded 28783684 bytes...
 [85%] Downloaded 28800004 bytes...
 [85%] Downloaded 28816388 bytes...
 [85%] Downloaded 28832708 bytes...
 [85%] Downloaded 28849092 bytes...
 [85%] Downloaded 28865412 bytes...
 [85%] Downloaded 28881796 bytes...
 [85%] Downloaded 28898116 bytes...
 [85%] Downloaded 28914500 bytes...
 [85%] Downloaded 28930820 bytes...
 [85%] Downloaded 28947204 bytes...
 [85%] Downloaded 28963524 bytes...
 [85%] Downloaded 28979908 bytes...
 [85%] Downloaded 28996228 bytes...
 [86%] Downloaded 29012612 bytes...
 [86%] Downloaded 29028932 bytes...
 [86%] Downloaded 29045316 bytes...
 [86%] Downloaded 29061636 bytes...
 [86%] Downloaded 29078020 bytes...
 [86%] Downloaded 29094340 bytes...
 [86%] Downloaded 29110724 bytes...
 [86%] Downloaded 29127044 bytes...
 [86%] Downloaded 29143428 bytes...
 [86%] Downloaded 29159748 bytes...
 [86%] Downloaded 29176132 bytes...
 [86%] Downloaded 29192452 bytes...
 [86%] Downloaded 29208836 bytes...
 [86%] Downloaded 29225156 bytes...
 [86%] Downloaded 29241540 bytes...
 [86%] Downloaded 29257860 bytes...
 [86%] Downloaded 29274244 bytes...
 [86%] Downloaded 29290564 bytes...
 [86%] Downloaded 29306948 bytes...
 [86%] Downloaded 29323268 bytes...
 [86%] Downloaded 29339652 bytes...
 [87%] Downloaded 29355972 bytes...
 [87%] Downloaded 29372356 bytes...
 [87%] Downloaded 29388676 bytes...
 [87%] Downloaded 29405060 bytes...
 [87%] Downloaded 29421380 bytes...
 [87%] Downloaded 29437764 bytes...
 [87%] Downloaded 29454084 bytes...
 [87%] Downloaded 29470468 bytes...
 [87%] Downloaded 29486788 bytes...
 [87%] Downloaded 29503172 bytes...
 [87%] Downloaded 29519492 bytes...
 [87%] Downloaded 29535876 bytes...
 [87%] Downloaded 29552196 bytes...
 [87%] Downloaded 29568580 bytes...
 [87%] Downloaded 29584900 bytes...
 [87%] Downloaded 29601284 bytes...
 [87%] Downloaded 29617604 bytes...
 [87%] Downloaded 29633988 bytes...
 [87%] Downloaded 29650308 bytes...
 [87%] Downloaded 29666692 bytes...
 [88%] Downloaded 29683012 bytes...
 [88%] Downloaded 29699396 bytes...
 [88%] Downloaded 29715716 bytes...
 [88%] Downloaded 29732100 bytes...
 [88%] Downloaded 29748420 bytes...
 [88%] Downloaded 29748436 bytes...
 [88%] Downloaded 29764820 bytes...
 [88%] Downloaded 29764868 bytes...
 [88%] Downloaded 29781132 bytes...
 [88%] Downloaded 29797516 bytes...
 [88%] Downloaded 29813836 bytes...
 [88%] Downloaded 29830220 bytes...
 [88%] Downloaded 29846540 bytes...
 [88%] Downloaded 29862924 bytes...
 [88%] Downloaded 29879244 bytes...
 [88%] Downloaded 29895628 bytes...
 [88%] Downloaded 29911948 bytes...
 [88%] Downloaded 29928332 bytes...
 [88%] Downloaded 29944652 bytes...
 [88%] Downloaded 29944668 bytes...
 [88%] Downloaded 29961052 bytes...
 [88%] Downloaded 29961100 bytes...
 [88%] Downloaded 29977364 bytes...
 [88%] Downloaded 29993748 bytes...
 [88%] Downloaded 30010068 bytes...
 [89%] Downloaded 30026452 bytes...
 [89%] Downloaded 30042772 bytes...
 [89%] Downloaded 30059156 bytes...
 [89%] Downloaded 30075476 bytes...
 [89%] Downloaded 30091860 bytes...
 [89%] Downloaded 30108180 bytes...
 [89%] Downloaded 30124564 bytes...
 [89%] Downloaded 30140884 bytes...
 [89%] Downloaded 30157268 bytes...
 [89%] Downloaded 30173588 bytes...
 [89%] Downloaded 30173604 bytes...
 [89%] Downloaded 30189988 bytes...
 [89%] Downloaded 30190036 bytes...
 [89%] Downloaded 30206300 bytes...
 [89%] Downloaded 30222684 bytes...
 [89%] Downloaded 30239004 bytes...
 [89%] Downloaded 30255388 bytes...
 [89%] Downloaded 30271708 bytes...
 [89%] Downloaded 30288092 bytes...
 [89%] Downloaded 30304412 bytes...
 [89%] Downloaded 30320796 bytes...
 [89%] Downloaded 30337116 bytes...
 [89%] Downloaded 30353500 bytes...
 [90%] Downloaded 30369820 bytes...
 [90%] Downloaded 30369836 bytes...
 [90%] Downloaded 30386220 bytes...
 [90%] Downloaded 30386268 bytes...
 [90%] Downloaded 30402532 bytes...
 [90%] Downloaded 30418916 bytes...
 [90%] Downloaded 30435236 bytes...
 [90%] Downloaded 30451620 bytes...
 [90%] Downloaded 30467940 bytes...
 [90%] Downloaded 30484324 bytes...
 [90%] Downloaded 30500644 bytes...
 [90%] Downloaded 30517028 bytes...
 [90%] Downloaded 30533348 bytes...
 [90%] Downloaded 30549732 bytes...
 [90%] Downloaded 30566052 bytes...
 [90%] Downloaded 30566068 bytes...
 [90%] Downloaded 30582452 bytes...
 [90%] Downloaded 30582500 bytes...
 [90%] Downloaded 30598764 bytes...
 [90%] Downloaded 30615148 bytes...
 [90%] Downloaded 30631468 bytes...
 [90%] Downloaded 30647852 bytes...
 [90%] Downloaded 30664172 bytes...
 [90%] Downloaded 30680556 bytes...
 [91%] Downloaded 30696876 bytes...
 [91%] Downloaded 30713260 bytes...
 [91%] Downloaded 30729580 bytes...
 [91%] Downloaded 30745964 bytes...
 [91%] Downloaded 30762284 bytes...
 [91%] Downloaded 30778668 bytes...
 [91%] Downloaded 30794988 bytes...
 [91%] Downloaded 30795004 bytes...
 [91%] Downloaded 30811388 bytes...
 [91%] Downloaded 30811436 bytes...
 [91%] Downloaded 30827700 bytes...
 [91%] Downloaded 30844084 bytes...
 [91%] Downloaded 30860404 bytes...
 [91%] Downloaded 30876788 bytes...
 [91%] Downloaded 30893108 bytes...
 [91%] Downloaded 30909492 bytes...
 [91%] Downloaded 30925812 bytes...
 [91%] Downloaded 30942196 bytes...
 [91%] Downloaded 30958516 bytes...
 [91%] Downloaded 30974900 bytes...
 [91%] Downloaded 30991220 bytes...
 [91%] Downloaded 30991236 bytes...
 [91%] Downloaded 31007620 bytes...
 [91%] Downloaded 31007668 bytes...
 [91%] Downloaded 31023932 bytes...
 [92%] Downloaded 31040316 bytes...
 [92%] Downloaded 31056636 bytes...
 [92%] Downloaded 31073020 bytes...
 [92%] Downloaded 31089340 bytes...
 [92%] Downloaded 31105724 bytes...
 [92%] Downloaded 31122044 bytes...
 [92%] Downloaded 31138428 bytes...
 [92%] Downloaded 31154748 bytes...
 [92%] Downloaded 31171132 bytes...
 [92%] Downloaded 31187452 bytes...
 [92%] Downloaded 31187468 bytes...
 [92%] Downloaded 31203852 bytes...
 [92%] Downloaded 31203900 bytes...
 [92%] Downloaded 31220164 bytes...
 [92%] Downloaded 31236548 bytes...
 [92%] Downloaded 31252868 bytes...
 [92%] Downloaded 31269252 bytes...
 [92%] Downloaded 31285572 bytes...
 [92%] Downloaded 31301956 bytes...
 [92%] Downloaded 31318276 bytes...
 [92%] Downloaded 31334660 bytes...
 [92%] Downloaded 31350980 bytes...
 [92%] Downloaded 31367364 bytes...
 [93%] Downloaded 31383684 bytes...
 [93%] Downloaded 31383700 bytes...
 [93%] Downloaded 31400084 bytes...
 [93%] Downloaded 31400132 bytes...
 [93%] Downloaded 31416396 bytes...
 [93%] Downloaded 31432780 bytes...
 [93%] Downloaded 31449100 bytes...
 [93%] Downloaded 31465484 bytes...
 [93%] Downloaded 31481804 bytes...
 [93%] Downloaded 31498188 bytes...
 [93%] Downloaded 31514508 bytes...
 [93%] Downloaded 31530892 bytes...
 [93%] Downloaded 31547212 bytes...
 [93%] Downloaded 31563596 bytes...
 [93%] Downloaded 31579916 bytes...
 [93%] Downloaded 31596300 bytes...
 [93%] Downloaded 31612620 bytes...
 [93%] Downloaded 31612636 bytes...
 [93%] Downloaded 31629020 bytes...
 [93%] Downloaded 31629068 bytes...
 [93%] Downloaded 31645332 bytes...
 [93%] Downloaded 31661716 bytes...
 [93%] Downloaded 31678036 bytes...
 [93%] Downloaded 31694420 bytes...
 [94%] Downloaded 31710740 bytes...
 [94%] Downloaded 31727124 bytes...
 [94%] Downloaded 31743444 bytes...
 [94%] Downloaded 31759828 bytes...
 [94%] Downloaded 31776148 bytes...
 [94%] Downloaded 31792532 bytes...
 [94%] Downloaded 31808852 bytes...
 [94%] Downloaded 31825236 bytes...
 [94%] Downloaded 31841556 bytes...
 [94%] Downloaded 31857940 bytes...
 [94%] Downloaded 31874260 bytes...
 [94%] Downloaded 31890644 bytes...
 [94%] Downloaded 31906964 bytes...
 [94%] Downloaded 31923348 bytes...
 [94%] Downloaded 31939668 bytes...
 [94%] Downloaded 31956052 bytes...
 [94%] Downloaded 31972372 bytes...
 [94%] Downloaded 31988756 bytes...
 [94%] Downloaded 32005076 bytes...
 [94%] Downloaded 32021460 bytes...
 [94%] Downloaded 32037780 bytes...
 [94%] Downloaded 32037796 bytes...
 [95%] Downloaded 32054180 bytes...
 [95%] Downloaded 32054228 bytes...
 [95%] Downloaded 32070492 bytes...
 [95%] Downloaded 32086876 bytes...
 [95%] Downloaded 32103196 bytes...
 [95%] Downloaded 32119580 bytes...
 [95%] Downloaded 32135900 bytes...
 [95%] Downloaded 32152284 bytes...
 [95%] Downloaded 32168604 bytes...
 [95%] Downloaded 32184988 bytes...
 [95%] Downloaded 32201308 bytes...
 [95%] Downloaded 32217692 bytes...
 [95%] Downloaded 32234012 bytes...
 [95%] Downloaded 32250396 bytes...
 [95%] Downloaded 32266716 bytes...
 [95%] Downloaded 32283100 bytes...
 [95%] Downloaded 32299420 bytes...
 [95%] Downloaded 32315804 bytes...
 [95%] Downloaded 32332124 bytes...
 [95%] Downloaded 32348508 bytes...
 [95%] Downloaded 32364828 bytes...
 [95%] Downloaded 32381212 bytes...
 [96%] Downloaded 32397532 bytes...
 [96%] Downloaded 32413916 bytes...
 [96%] Downloaded 32430236 bytes...
 [96%] Downloaded 32446620 bytes...
 [96%] Downloaded 32462940 bytes...
 [96%] Downloaded 32479324 bytes...
 [96%] Downloaded 32495644 bytes...
 [96%] Downloaded 32512028 bytes...
 [96%] Downloaded 32528348 bytes...
 [96%] Downloaded 32544732 bytes...
 [96%] Downloaded 32561052 bytes...
 [96%] Downloaded 32577436 bytes...
 [96%] Downloaded 32593756 bytes...
 [96%] Downloaded 32610140 bytes...
 [96%] Downloaded 32626460 bytes...
 [96%] Downloaded 32642844 bytes...
 [96%] Downloaded 32659164 bytes...
 [96%] Downloaded 32675548 bytes...
 [96%] Downloaded 32691868 bytes...
 [96%] Downloaded 32708252 bytes...
 [97%] Downloaded 32724572 bytes...
 [97%] Downloaded 32740956 bytes...
 [97%] Downloaded 32757276 bytes...
 [97%] Downloaded 32757292 bytes...
 [97%] Downloaded 32773676 bytes...
 [97%] Downloaded 32773724 bytes...
 [97%] Downloaded 32789988 bytes...
 [97%] Downloaded 32806372 bytes...
 [97%] Downloaded 32822692 bytes...
 [97%] Downloaded 32839076 bytes...
 [97%] Downloaded 32855396 bytes...
 [97%] Downloaded 32871780 bytes...
 [97%] Downloaded 32888100 bytes...
 [97%] Downloaded 32904484 bytes...
 [97%] Downloaded 32920804 bytes...
 [97%] Downloaded 32937188 bytes...
 [97%] Downloaded 32953508 bytes...
 [97%] Downloaded 32969892 bytes...
 [97%] Downloaded 32986212 bytes...
 [97%] Downloaded 33002596 bytes...
 [97%] Downloaded 33018916 bytes...
 [97%] Downloaded 33035300 bytes...
 [97%] Downloaded 33051620 bytes...
 [98%] Downloaded 33068004 bytes...
 [98%] Downloaded 33084324 bytes...
 [98%] Downloaded 33100708 bytes...
 [98%] Downloaded 33117028 bytes...
 [98%] Downloaded 33133412 bytes...
 [98%] Downloaded 33149732 bytes...
 [98%] Downloaded 33166116 bytes...
 [98%] Downloaded 33182436 bytes...
 [98%] Downloaded 33198820 bytes...
 [98%] Downloaded 33215140 bytes...
 [98%] Downloaded 33231524 bytes...
 [98%] Downloaded 33247844 bytes...
 [98%] Downloaded 33264228 bytes...
 [98%] Downloaded 33280548 bytes...
 [98%] Downloaded 33296932 bytes...
 [98%] Downloaded 33313252 bytes...
 [98%] Downloaded 33329636 bytes...
 [98%] Downloaded 33345956 bytes...
 [98%] Downloaded 33362340 bytes...
 [98%] Downloaded 33378660 bytes...
 [99%] Downloaded 33395044 bytes...
 [99%] Downloaded 33411364 bytes...
 [99%] Downloaded 33427748 bytes...
 [99%] Downloaded 33444068 bytes...
 [99%] Downloaded 33460452 bytes...
 [99%] Downloaded 33476772 bytes...
 [99%] Downloaded 33493156 bytes...
 [99%] Downloaded 33509476 bytes...
 [99%] Downloaded 33525860 bytes...
 [99%] Downloaded 33542180 bytes...
 [99%] Downloaded 33558564 bytes...
 [99%] Downloaded 33574884 bytes...
 [99%] Downloaded 33591268 bytes...
 [99%] Downloaded 33607588 bytes...
 [99%] Downloaded 33623972 bytes...
 [99%] Downloaded 33640292 bytes...
 [99%] Downloaded 33656676 bytes...
 [99%] Downloaded 33672996 bytes...
 [99%] Downloaded 33689380 bytes...
 [99%] Downloaded 33705700 bytes...
 [99%] Downloaded 33722084 bytes...
 [100%] Downloaded 33730584 bytes...
msigdbr_t2g <- go_gene_sets %>% dplyr::distinct(gs_name,gene_symbol) %>% as.data.frame() # make a dataframe of the genesets and the corresponding Ensemble gene ids

Load the DE results file and subset for significantly upregulated genes

DE.res <- read.csv("DE_sensitiveVSresistant_results_wGeneSymbol.csv", header = TRUE, row.names = 1)
DE.res.sign <- subset(DE.res, padj < 0.05 & log2FoldChange > 1)

Perform enrichment analysis and write results in a .csv file

enrichRes <- enricher(gene = DE.res.sign$gene.symbol, TERM2GENE = msigdbr_t2g, pvalueCutoff = 0.05, pAdjustMethod = "BH")
write.csv(enrichRes@result, file = "GO_sensitiveVSresistant_up.csv", row.names = FALSE)
head(enrichRes)

Pre-ranked GSEA

Installing packages

#BiocManager::install("fgsea")
library(fgsea)

#install.packages("data.table")
library(data.table)

BiocManager::install("qusage")
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")'
for details.
Replacement repositories:
    CRAN: https://cran.rstudio.com/
Bioconductor version 3.15 (BiocManager 1.30.26), R 4.2.3 (2023-03-15)
Installing package(s) 'qusage'
also installing the dependencies ‘estimability’, ‘mvtnorm’, ‘emmeans’, ‘fftw’

Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.15/data/annotation/bin/macosx/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.15/data/annotation/bin/macosx/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.15/data/experiment/bin/macosx/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.15/data/experiment/bin/macosx/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.15/workflows/bin/macosx/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.15/workflows/bin/macosx/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 11573Warning: cannot open URL 'https://bioconductor.org/packages/3.15/books/bin/macosx/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 11573Warning: cannot open URL 'https://bioconductor.org/packages/3.15/books/bin/macosx/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'

  There are binary versions available but the source versions are later:
no
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/mvtnorm_1.2-4.tgz'
Content type 'application/x-gzip' length 796467 bytes (777 KB)
==================================================
downloaded 777 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/fftw_1.0-7.tgz'
Content type 'application/x-gzip' length 475876 bytes (464 KB)
==================================================
downloaded 464 KB

trying URL 'https://bioconductor.org/packages/3.15/bioc/bin/macosx/contrib/4.2/qusage_2.30.0.tgz'
Content type 'application/x-compressed-tar' length 10290241 bytes (9.8 MB)
==================================================
downloaded 9.8 MB

The downloaded binary packages are in
    /var/folders/db/_9mqvxh50pb53z2xy8z_xhjr0000gn/T//Rtmp173bOF/downloaded_packages
installing the source packages ‘estimability’, ‘emmeans’

trying URL 'https://cran.rstudio.com/src/contrib/estimability_1.5.1.tar.gz'
Content type 'application/x-gzip' length 15968 bytes (15 KB)
==================================================
downloaded 15 KB

trying URL 'https://cran.rstudio.com/src/contrib/emmeans_1.11.2.tar.gz'
Content type 'application/x-gzip' length 1521215 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

* installing *source* package ‘estimability’ ...
** package ‘estimability’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (estimability)
* installing *source* package ‘emmeans’ ...
** package ‘emmeans’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (emmeans)

The downloaded source packages are in
    ‘/private/var/folders/db/_9mqvxh50pb53z2xy8z_xhjr0000gn/T/Rtmp173bOF/downloaded_packages’
Old packages: 'ape', 'brio', 'curl', 'data.table', 'diffobj', 'fastmatch', 'fftw', 'gert', 'ggforce', 'ggraph',
  'ggrepel', 'graphlayouts', 'igraph', 'KernSmooth', 'mclust', 'mvtnorm', 'nlme', 'openssl', 'polyclip', 'processx',
  'profvis', 'ps', 'purrr', 'ragg', 'RcppArmadillo', 'RCurl', 'restfulr', 'roxygen2', 'S7', 'systemfonts', 'testthat',
  'textshaping', 'tidygraph', 'tweenr', 'XML', 'zip'
Update all/some/none? [a/s/n]: 
a
Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.15/data/annotation/bin/macosx/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.15/data/annotation/bin/macosx/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.15/data/experiment/bin/macosx/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.15/data/experiment/bin/macosx/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.15/workflows/bin/macosx/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 250Warning: cannot open URL 'https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.15/workflows/bin/macosx/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 11573Warning: cannot open URL 'https://bioconductor.org/packages/3.15/books/bin/macosx/contrib/4.2/PACKAGES.rds': HTTP status was '404 Not Found'Warning: downloaded length 0 != reported length 11573Warning: cannot open URL 'https://bioconductor.org/packages/3.15/books/bin/macosx/contrib/4.2/PACKAGES.gz': HTTP status was '404 Not Found'

  There are binary versions available but the source versions are later:
no
trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/ape_5.7-1.tgz'
Content type 'application/x-gzip' length 3479252 bytes (3.3 MB)
==================================================
downloaded 3.3 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/brio_1.1.4.tgz'
Content type 'application/x-gzip' length 42717 bytes (41 KB)
==================================================
downloaded 41 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/curl_5.2.0.tgz'
Content type 'application/x-gzip' length 791519 bytes (772 KB)
==================================================
downloaded 772 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/data.table_1.14.10.tgz'
Content type 'application/x-gzip' length 2343663 bytes (2.2 MB)
==================================================
downloaded 2.2 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/diffobj_0.3.5.tgz'
Content type 'application/x-gzip' length 1004587 bytes (981 KB)
==================================================
downloaded 981 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/fastmatch_1.1-4.tgz'
Content type 'application/x-gzip' length 50284 bytes (49 KB)
==================================================
downloaded 49 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/fftw_1.0-7.tgz'
Content type 'application/x-gzip' length 475876 bytes (464 KB)
==================================================
downloaded 464 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/gert_2.0.1.tgz'
Content type 'application/x-gzip' length 1998048 bytes (1.9 MB)
==================================================
downloaded 1.9 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/ggforce_0.4.1.tgz'
Content type 'application/x-gzip' length 4534238 bytes (4.3 MB)
==================================================
downloaded 4.3 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/ggraph_2.1.0.tgz'
Content type 'application/x-gzip' length 4652466 bytes (4.4 MB)
==================================================
downloaded 4.4 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/ggrepel_0.9.4.tgz'
Content type 'application/x-gzip' length 578404 bytes (564 KB)
==================================================
downloaded 564 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/graphlayouts_1.0.1.tgz'
Content type 'application/x-gzip' length 4537326 bytes (4.3 MB)
==================================================
downloaded 4.3 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/igraph_1.5.1.tgz'
Content type 'application/x-gzip' length 8627201 bytes (8.2 MB)
==================================================
downloaded 8.2 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/KernSmooth_2.23-22.tgz'
Content type 'application/x-gzip' length 100525 bytes (98 KB)
==================================================
downloaded 98 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/mclust_6.0.1.tgz'
Content type 'application/x-gzip' length 4237708 bytes (4.0 MB)
==================================================
downloaded 4.0 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/mvtnorm_1.2-4.tgz'
Content type 'application/x-gzip' length 796467 bytes (777 KB)
==================================================
downloaded 777 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/nlme_3.1-164.tgz'
Content type 'application/x-gzip' length 2404341 bytes (2.3 MB)
==================================================
downloaded 2.3 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/openssl_2.1.1.tgz'
Content type 'application/x-gzip' length 2886259 bytes (2.8 MB)
==================================================
downloaded 2.8 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/polyclip_1.10-6.tgz'
Content type 'application/x-gzip' length 465379 bytes (454 KB)
==================================================
downloaded 454 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/processx_3.8.3.tgz'
Content type 'application/x-gzip' length 312250 bytes (304 KB)
==================================================
downloaded 304 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/profvis_0.3.8.tgz'
Content type 'application/x-gzip' length 200631 bytes (195 KB)
==================================================
downloaded 195 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/ps_1.7.5.tgz'
Content type 'application/x-gzip' length 308891 bytes (301 KB)
==================================================
downloaded 301 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/purrr_1.0.2.tgz'
Content type 'application/x-gzip' length 510913 bytes (498 KB)
==================================================
downloaded 498 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/ragg_1.2.7.tgz'
Content type 'application/x-gzip' length 9236153 bytes (8.8 MB)
==================================================
downloaded 8.8 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/RcppArmadillo_0.12.6.6.1.tgz'
Content type 'application/x-gzip' length 1613879 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/RCurl_1.98-1.13.tgz'
Content type 'application/x-gzip' length 1092020 bytes (1.0 MB)
==================================================
downloaded 1.0 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/restfulr_0.0.15.tgz'
Content type 'application/x-gzip' length 347166 bytes (339 KB)
==================================================
downloaded 339 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/roxygen2_7.2.3.tgz'
Content type 'application/x-gzip' length 910190 bytes (888 KB)
==================================================
downloaded 888 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/S7_0.1.1.tgz'
Content type 'application/x-gzip' length 278131 bytes (271 KB)
==================================================
downloaded 271 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/systemfonts_1.0.5.tgz'
Content type 'application/x-gzip' length 5898277 bytes (5.6 MB)
==================================================
downloaded 5.6 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/testthat_3.2.1.tgz'
Content type 'application/x-gzip' length 3100512 bytes (3.0 MB)
==================================================
downloaded 3.0 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/textshaping_0.3.7.tgz'
Content type 'application/x-gzip' length 5354762 bytes (5.1 MB)
==================================================
downloaded 5.1 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/tidygraph_1.3.0.tgz'
Content type 'application/x-gzip' length 632444 bytes (617 KB)
==================================================
downloaded 617 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/tweenr_2.0.2.tgz'
Content type 'application/x-gzip' length 783938 bytes (765 KB)
==================================================
downloaded 765 KB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/XML_3.99-0.16.tgz'
Content type 'application/x-gzip' length 1868841 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.2/zip_2.3.0.tgz'
Content type 'application/x-gzip' length 211400 bytes (206 KB)
==================================================
downloaded 206 KB

The downloaded binary packages are in
    /var/folders/db/_9mqvxh50pb53z2xy8z_xhjr0000gn/T//Rtmp173bOF/downloaded_packages
library(qusage)
Loading required package: limma

Attaching package: ‘qusage’

The following object is masked from ‘package:clusterProfiler’:

    read.gmt
#install.packages("ggplot2")
library(ggplot2)

Load the Gene Set collection (Note you need to download the gmt file of the collection of your interest from MSigDB)

gmt.file <- read.gmt("c5.go.bp.v7.4.symbols.gmt")

Ranking our DE results

DE.res.ranked <- DE.res[order(DE.res$log2FoldChange, decreasing = T), ]

DE.ranks <- setNames(DE.res.ranked$log2FoldChange, DE.res.ranked$gene.symbol) # creating a named vector of the ranks

Running fgsea


fgseaRes <- fgsea(gmt.file, DE.ranks, minSize=15, maxSize=500)
Warning: There are duplicate gene names, fgsea may produce unexpected results.
# writing the results into a file
fwrite(fgseaRes, file = "PrerankedGSEA_gobp_sensitiveVSresistant.txt", sep = "\t", sep2=c("", " ", ""))

Producing an enrichment plot

topPathways <- fgseaRes[order(padj)][padj <= 0.05]$pathway
EnPlot <- plotEnrichment(gmt.file[["GOBP_EPITHELIUM_DEVELOPMENT"]],DE.ranks) + labs(title="GOBP_EPITHELIUM_DEVELOPMENT") + theme(text = element_text(size=20))
EnPlot2 <- plotEnrichment(gmt.file[["GOBP_OXIDATIVE_PHOSPHORYLATION"]],DE.ranks) + labs(title="GOBP_OXIDATIVE_PHOSPHORYLATION") + theme(text = element_text(size=20))

EnPlot

EnPlot2

X-axis (“rank”): Genes ranked from most upregulated (left) to most downregulated (right) based on a metric (e.g., log2FC, signal-to-noise).

Black ticks: Locations of genes from the epithelium development gene set along the ranked gene list.

Green curve: The enrichment score (ES) — it reflects how concentrated the gene set is near the top (left) or bottom (right) of the ranked list.

If the peak is on the left: gene set is enriched in upregulated genes.

If on the right: enriched in downregulated genes.

Red dashed lines: Indicate the range of observed ES scores; useful for permutation testing.

✅ Interpretation of your plot: The green line peaks early, around the left side of the ranked gene list.

This indicates that genes in the GOBP_EPITHELIUM_DEVELOPMENT gene set are enriched at the top of the ranking.

Therefore, this gene set is upregulated (i.e., activated or associated) in your chemo-sensitive group (if that’s the direction of the ranking).

🧠 Biological interpretation: Epithelium development–related genes are significantly enriched among the most upregulated genes in your condition (likely chemo-sensitive).

This may suggest that epithelial differentiation or maintenance is more active in chemo-sensitive samples.

---
title: "RNA seq Workflow with DeSEQ"
output: html_notebook
---
```{r}
getwd()
```
```{r}
knitr::opts_chunk$set(echo = TRUE)
```

```{r}
 if (!requireNamespace("BiocManager", quietly = TRUE))
     install.packages("BiocManager")
BiocManager::install("DESeq2", version = "3.14")

```
BiocManager::install("pheatmap")


# RNA-seq Analysis

workflow: raw counts -> normalization -> unsupervised clustering (PCA) -> DE analysis -> shrinking log2 fold change -> results exploration
- can add more downstream analysis as well

```{r}
BiocManager::install("pheatmap")
```

#dependencies
```{r}
library(DESeq2)
library(pheatmap)
```
# Preprocessing
## Reading and rounding the values of raw counts file (geneid x sample names)
```{r}
## Loading Input files and creating DESeq2 object
raw_counts <- read.delim("counts.txt", header = T, row.names = 1)
raw_counts <- ceiling(raw_counts) #round them up to integers
head(raw_counts)
```
## Loading metadata
```{r}
meta_data <- read.delim("sampleGroups.txt", header = T, row.names = 1)
head(meta_data)
```
If the row names of metadata and col names of raw counts data:
idx <- match(rownames(metadata), colnames(rawcounts))
and apply the idx to the desired data to be reordered.

## Modelling DeSeq2 Object
```{r}
dds <- DESeqDataSetFromMatrix(countData = raw_counts,
                              colData = meta_data,
                              design = ~group) #group is the condition:resistant or sensitive in this case
dds
```

## Filter out low gene counts
```{r}
keep <- rowSums(counts(dds) >= 10) >= 3
dds <- dds[keep,]

```

counts(dds) -> gets the count matrix
rowSums() -> for each gene counts the samples that are over 10

## DE Analysis
```{r}
dds <- DESeq(dds)
```


## Normalization and Log Transformation (transformed counts)
```{r}
#estimateSizeFactors(dds)
#sizeFactors(dds)

#normalization
norm.counts <- counts(dds, normalized = TRUE) #normalize the counts for accuracy
write.csv(norm.counts, file = "normalized_counts.txt", row.names = TRUE)
head(norm.counts)

#log transformation, transformed counts
vsd <- vst(dds, blind = FALSE) 

#creating as a matrix
vsd_matrix <- assay(vsd)
head(vsd_matrix)
```
## Adding correlation to log transformation
```{r}
vsd_cor <- cor(vsd_matrix) #applies correlation for a pheatmap
head(vsd_cor)
vsd_cor <- data.frame(vsd_cor)

pheatmap(vsd_cor, annotation = select(meta_data, group))
```
1 indicates strong correlation - shows a good biological relevance.
- Same groups have correlation of 1.

This plot supports that:
- Chemo-sensitive and chemo-resistant samples have distinct gene expression profiles -> distinct transcriptomic level.
- The clustering and correlation structure suggest clear biological separation, which is a good foundation for further differential expression or biomarker analysis.

## Unsupervised Clustering
```{r}
plotPCA(vsd, intgroup = c("group")) # does not want the matrix version
```
- PC1 explains 87% of the variance — this is the main axis separating your samples.
- Clear separation between two group -> This suggests strong transcriptomic differences between the two groups.
- PC2 (8% variance) captures minor variation within groups.

## Hierarchical Clustering
```{r}
#plotting hierarchical clustering using vst transformed counts
sampleDists <- dist(t(assay(vsd)))
plot(hclust(sampleDists, method = "complete"))
```

## Plot dispersion estimates -- used DESeq2 object
```{r}
mean.counts <- apply(raw_counts[,1:3],1,mean)

var.counts <- apply(raw_counts[,1:3],1,var)

# Plot dispersion estimates to visualize variability in gene expression
# - Black dots: raw gene-wise dispersion estimates (highly variable for low-count genes)
# - Red line: fitted trend showing expected dispersion based on mean counts
# - Blue dots: final dispersion values used in the model (shrunken for stability)
# This plot helps assess whether DESeq2's dispersion modeling and shrinkage worked correctly

plotDispEsts(dds) 

```

# Key observation:
 - Low-count genes (left) have high raw dispersion, but shrinkage pulls them toward the red trend line.
 - High-count genes (right) show less variability and need minimal shrinkage.
This confirms DESeq2's dispersion estimation and shrinkage worked correctly, improving statistical robustness.
• As mean counts increase, raw dispersions are more stable; blue ≈ black (less shrinkage needed).
• Overall fit looks good (no strong systematic deviations), so dispersion modeling succeeded and you can confidently proceed to differential expression testing.

## Get DE results
```{r}
dds.res <- results(dds, contrast = c("group","chemo_sensitive", "chemo_resistant"), alpha = 0.05)
summary(dds.res)
mcols(dds.res)$description

write.csv(as.data.frame(dds.res), file="DE_sensitiveVSresistant_results.csv")
```
Summary of Differential Expression Results:
- 18,577 genes had a nonzero total read count (i.e., were expressed in at least one sample).
- 2,156 genes were upregulated in chemo_sensitive vs chemo_resistant (12%).
- 1,875 genes were downregulated (10%).
- This means ~22% of all expressed genes are significantly different between the two conditions.
- 8 genes (0.043%) were flagged as outliers due to extreme values (checked using Cook’s distance).
- 0 genes were filtered out due to low mean counts (<6), likely because of independent filtering.

```{r}
plotMA(dds.res)
```
- LFC > 0 is up-regulated genes; LFC < 0 is down-regulated genes.
- Grey points are the genes that are not statistically significant.
- Blue points genes with p.adj < 0.05 (significantly differentially expressed)
- There is a large number of significantly differentially expressed genes, especially in genes with moderate-to-high expression (middle x-axis).
- The triangle markers suggest some genes have very large fold changes and may be biologically interesting.

## Volcano Plot
```{r}
BiocManager::install('EnhancedVolcano')
library(EnhancedVolcano)
```

```{r}
EnhancedVolcano(dds.res,
    lab = rownames(dds.res),
    x = 'log2FoldChange',
    y = 'padj')
```
- genes to the right are up-regulated due to LFC > 0
- genes to the left are down-regulated due to LFC < 0
- higher values are more statisticaly significant
- There are many red points, meaning a large number of genes show both statistically significant changes and large expression differences between the two conditions.
- The volcano plot confirms the biological distinction between chemo-sensitive and resistant samples.
- Genes near the center LFC~0 are not statistically significant.

## Most significant DE genes
```{r}
plotCounts(dds, gene=which.min(dds.res$padj), intgroup="group")
# the lowest padj indicates the most significant gene
```
## Visualizing expression data with a heatmap
```{r}
# extracting significantly DE genes -- padj < 0.05 & abs(lfc) > 1
# thresholding for significanlty differentially expressed genes with at least two-ford change in expression
de.sign <- subset(dds.res, padj < 0.05 & abs(log2FoldChange) > 1)

# creating a vector of Ensembl id for those genes
de.sign.genes <- rownames(de.sign)

# subseting the vsd matrix to include only the de.sign.genes and scaling it by row so that we plot on the heatmap
scale.dat <- t(scale(t(assay(vsd)[de.sign.genes,])))
pheatmap(scale.dat[de.sign.genes,], cluster_rows=TRUE, show_rownames=FALSE, cluster_cols=TRUE)
```

## Annotating DE Results

```{r}
BiocManager::install('AnnotationDbi')
BiocManager::install("org.Hs.eg.db")
library(AnnotationDbi)
library(org.Hs.eg.db)
```
```{r}
res.df <- as.data.frame(dds.res) # putting the de.sign into a data.frame to help the next step to work
res.annot <- mapIds(org.Hs.eg.db, keys = rownames(res.df), keytype = "ENSEMBL", column = "SYMBOL") #mapping ensembl ids to Gene Symbols

res.df.annot <- cbind(res.df,gene.symbol = res.annot) #binding the annotations to the sign.df

head(res.df.annot)

write.csv(res.df.annot, file = "DE_sensitiveVSresistant_results_wGeneSymbol.csv")
```
```{r}
EnhancedVolcano(res.df.annot,
    lab = res.df.annot$gene.symbol,
    x = 'log2FoldChange',
    y = 'padj')
```

# Over-representation test
## Install R packages and load libraries
```{r}
BiocManager::install("clusterProfiler")
library(clusterProfiler)

install.packages("msigdbr")
library(msigdbr)
```
msigdbr is an R package that gives you easy access to gene sets from the Molecular Signatures Database (MSigDB) — a widely used resource for gene set enrichment analysis (GSEA).

## Load the C5 collection from MSigDB i.e. Gene Ontologies
```{r}
go_gene_sets <- msigdbr(species = "human", category = "C5")  #Load C5

msigdbr_t2g <- go_gene_sets %>% dplyr::distinct(gs_name,gene_symbol) %>% as.data.frame() # make a dataframe of the genesets and the corresponding Ensemble gene ids
#t processes a gene set data frame (likely created using msigdbr()), and formats it for enrichment analysis, especially for use with clusterProfiler::enricher().
```
## Load the DE results file and subset for significantly upregulated genes
```{r}
DE.res <- read.csv("DE_sensitiveVSresistant_results_wGeneSymbol.csv", header = TRUE, row.names = 1)
DE.res.sign <- subset(DE.res, padj < 0.05 & log2FoldChange > 1)
```

## Perform enrichment analysis and write results in a .csv file
```{r}
enrichRes <- enricher(gene = DE.res.sign$gene.symbol, TERM2GENE = msigdbr_t2g, pvalueCutoff = 0.05, pAdjustMethod = "BH")
write.csv(enrichRes@result, file = "GO_sensitiveVSresistant_up.csv", row.names = FALSE)
head(enrichRes)
```


# Pre-ranked GSEA
## Installing packages
```{r}
#BiocManager::install("fgsea")
library(fgsea)

#install.packages("data.table")
library(data.table)

BiocManager::install("qusage")
library(qusage)

#install.packages("ggplot2")
library(ggplot2)
```

## Load the Gene Set collection (Note you need to download the gmt file of the collection of your interest from MSigDB)
```{r}
gmt.file <- read.gmt("c5.go.bp.v7.4.symbols.gmt")
```

## Ranking our DE results
```{r}
DE.res.ranked <- DE.res[order(DE.res$log2FoldChange, decreasing = T), ]

DE.ranks <- setNames(DE.res.ranked$log2FoldChange, DE.res.ranked$gene.symbol) # creating a named vector of the ranks
```


## Running fgsea
```{r}

fgseaRes <- fgsea(gmt.file, DE.ranks, minSize=15, maxSize=500)

# writing the results into a file
fwrite(fgseaRes, file = "PrerankedGSEA_gobp_sensitiveVSresistant.txt", sep = "\t", sep2=c("", " ", ""))
```

## Producing an enrichment plot
```{r}
topPathways <- fgseaRes[order(padj)][padj <= 0.05]$pathway
EnPlot <- plotEnrichment(gmt.file[["GOBP_EPITHELIUM_DEVELOPMENT"]],DE.ranks) + labs(title="GOBP_EPITHELIUM_DEVELOPMENT") + theme(text = element_text(size=20))
EnPlot2 <- plotEnrichment(gmt.file[["GOBP_OXIDATIVE_PHOSPHORYLATION"]],DE.ranks) + labs(title="GOBP_OXIDATIVE_PHOSPHORYLATION") + theme(text = element_text(size=20))

EnPlot
EnPlot2

```
X-axis ("rank"):
Genes ranked from most upregulated (left) to most downregulated (right) based on a metric (e.g., log2FC, signal-to-noise).

Black ticks:
Locations of genes from the epithelium development gene set along the ranked gene list.

Green curve:
The enrichment score (ES) — it reflects how concentrated the gene set is near the top (left) or bottom (right) of the ranked list.

If the peak is on the left: gene set is enriched in upregulated genes.

If on the right: enriched in downregulated genes.

Red dashed lines:
Indicate the range of observed ES scores; useful for permutation testing.

✅ Interpretation of your plot:
The green line peaks early, around the left side of the ranked gene list.

This indicates that genes in the GOBP_EPITHELIUM_DEVELOPMENT gene set are enriched at the top of the ranking.

Therefore, this gene set is upregulated (i.e., activated or associated) in your chemo-sensitive group (if that's the direction of the ranking).

🧠 Biological interpretation:
Epithelium development–related genes are significantly enriched among the most upregulated genes in your condition (likely chemo-sensitive).

This may suggest that epithelial differentiation or maintenance is more active in chemo-sensitive samples.

